satarupa22/MacromolecularLigandDB huggingface dataset:
TTK kinase domain in complex with BAY 1217389 (PDB entry 5NAD)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHLVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.20593
R free: 0.28967
Average B factor: 89.214
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 293
Crystal growth procedure: 32 - 37% PEG400 (Acros, Geel, Belgium), 0.1 M Na/K phosphate pH 6.3 and 250 mM NaCl.pH 6.3
Matthews coefficient: 3.05
Solvent content (%): 59.7
Ligand: BAY 1217389 (8RH)
Ligand formula: C27 H24 F5 N5 O3
Ligand molecular weight: 561.503
Ligand SMILES: Cc1cc(ccc1C(=O)NC2CC2)c3cnc4n3nc(cc4NCCC(F)(F)F)Oc5ccc(c(c5F)F)OC
Ligand InChI: InChI=1S/C27H24F5N5O3/c1-14-11-15(3-6-17(14)26(38)35-16-4-5-16)19-13-34-25-18(33-10-9-27(30,31)32)12-22(36-37(19)25)40-21-8-7-20(39-2)23(28)24(21)29/h3,6-8,11-13,16,33H,4-5,9-10H2,1-2H3,(H,35,38)
Release date: 2017-05-31
Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide (PDB entry 7AKS)
Macromolecule: ADP-ribose glycohydrolase ARH3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 349 residues
Sequence: GPGSSLSRFRGCLAGALLGDCVGSFYAAHDTVDLTSVLRHVQSLEPDPGTPGSERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQKS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1685
R free: 0.1946
Average B factor: 29.039
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: sodium citrate (pH 6.1), 18% (w/v) PEG4000 and 400 mM ammonium acetate
Matthews coefficient: 2.51
Solvent content (%): 50.91
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2021-06-16
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000529a (PDB entry 7GT5)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.2002
R free: 0.2334
Average B factor: 37.549
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.34
Solvent content (%): 63.14
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Crystal structure of human glycogen branching enzyme (GBE1) in complex with maltoheptaose (PDB entry 5CLW)
Macromolecule: 1,4-alpha-glucan-branching enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.18
Sequence length: 668 residues
Sequence: YFQSMLKPYAVDFQRRYKQFSQILKNIGENEGGIDKFSRGYESFGVHRCADGGLYCKEWAPGAEGVFLTGDFNGWNPFSYPYKKLDYGKWELYIPPKQNKSVLVPHGSKLKVVITSKSGEILYRISPWAKYVVREGDNVNYDWIHWDPEHSYEFKHSRPKKPRSLRIYESHVGISSHEGKVASYKHFTCNVLPRIKGLGYNCIQLMAIMEHAYYASFGYQITSFFAASSRYGSPEELQELVDTAHSMGIIVLLDVVHSHASKNSADGLNMFDGTDSCYFHSGPRGTHDLWDSRLFAYSSWEVLRFLLSNIRWWLEEYRFDGFRFDGVTSMLYHHHGVGQGFSGDYSEYFGLQVDEDALTYLMLANHLVHTLCPDSITIAEDVSGMPALCSPISQGGGGFDYRLAMAIPDKWIQLLKEFKDEDWNMGDIVYTLTNRRYLEKCIAYAESHDQALVGDKSLAFWLMDAEMYTNMSVLTPFTPVIDRGIQLHKMIRLITHGLGGEGYLNFMGNEFGHPEWLDFPRKGNNESYHYARRQFHLTDDDLLRYKFLNNFDRDMNRLEERYGWLAAPQAYVSEKHEGNKIIAFERAGLLFIFNFHPSKSYTDYRVGTALPGKFKIVLDSDAAEYGGHQRLDHSTDFFSEAFEHNGRPYSLLVYIPSRVALILQNVDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1952
R free: 0.2312
Average B factor: 55.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG 3350 , 0.2M sodium succinate
Matthews coefficient: 3.25
Solvent content (%): 62.18
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-10-07
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z32327641 (PDB entry 5RWT)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1775
R free: 0.2037
Average B factor: 18.552
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.1
Solvent content (%): 41.57
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2020-11-11
Kinetic and Structural Changes in HsmtPheRS, Induced by Pathogenic Mutations in Human FARS2 (PDB entry 5MGW)
Macromolecule: Phenylalanine--tRNA ligase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.20
Sequence length: 406 residues
Sequence: APGSVVELLGKSYPQDDHSNLTRKVLTRVGRNLHNQQHHPLWLIKERVKEHFYKQYVGRFGTPLFSVYDNLSPVVTTWQNFDSLLIPADHPSRKKGDNYYLNRTHMLRAHTSAHQWDLLHAGLDAFLVVGDVYRRDQIDSQHYPIFHQLEAVRLFSKHELFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGEWLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSENYAENDFYDLVRTIGGDLVEKVDLIDKFVHPKTHKTSHCYRITYCHMERTLSQREVRHIHQALQEAAVQLLGVEGRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1851
R free: 0.2049
Average B factor: 28.2491
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 2 mM DTT, 100 mM bis-Tris propane pH 7 and 1.8 M sodium acetate pH 7
Matthews coefficient: 2.51
Solvent content (%): 50.96
Ligand: PHENYLALANINE (PHE)
Ligand formula: C9 H11 N O2
Ligand molecular weight: 165.189
Ligand SMILES: c1ccc(cc1)CC(C(=O)O)N
Ligand InChI: InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1
Release date: 2017-05-03
Notum Inhibitor ARUK3006561 (PDB entry 8BSQ)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1926
R free: 0.2001
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.94
Solvent content (%): 36.65
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2022-12-14
Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 3.0 mM Mn2+ for 600s (PDB entry 7U83)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1896
R free: 0.2321
Average B factor: 33.8148
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG2000 MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.12
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2022-05-04
Human Cyclophilin D in complex with bicyclic fragment (PDB entry 6R9S)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.162
R free: 0.2284
Average B factor: 14.44
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 298
Crystal growth procedure: 50 mM potassium phosphate
Matthews coefficient: 1.97
Solvent content (%): 37.47
Ligand: (1~{R},9~{R},10~{S})-4-fluoranyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-10-ol (JVN)
Ligand formula: C11 H12 F N O2
Ligand molecular weight: 209.217
Ligand SMILES: c1cc2c(cc1F)C3CC(N2)C(CO3)O
Ligand InChI: InChI=1S/C11H12FNO2/c12-6-1-2-8-7(3-6)11-4-9(13-8)10(14)5-15-11/h1-3,9-11,13-14H,4-5H2/t9-,10-,11-/m1/s1
Release date: 2019-11-27
ASH1L wild-type SET domain in complex with S-adenosyl methionine (SAM) (PDB entry 4YNM)
Macromolecule: Histone-lysine N-methyltransferase ASH1L
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 226 residues
Sequence: GAMAGSYKKIRSNVYVDVKPLSGYEATTCNCKKPDDDTRKGCVDDCLNRMIFAECSPNTCPCGEQCCNQRIQRHEWVQCLERFRAEEKGWGIRTKEPLKAGQFIIEYLGEVVSEQEFRNRMIEQYHNHSDHYCLNLDSGMVIDSYRMGNEARFINHSCDPNCEMQKWSVNGVYRIGLYALKDMPAGTELTYDYNFHSFNVEKQQLCKCGFEKCRGIIGGKSQRVNG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.2421
R free: 0.2775
Average B factor: 42.453
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350, 20 mM Tris
Matthews coefficient: 2.34
Solvent content (%): 47.41
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2015-09-02
Crystal structure of Protein Phosphatase 1 bound to the natural inhibitor Tautomycetin (PDB entry 6ALZ)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 299 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.208
R work: 0.1842
R free: 0.2158
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 6000, 1 M lithium chloride, 0.1 M Tris pH 8.0
Matthews coefficient: 2.56
Solvent content (%): 51.89
Ligand: (2Z)-2-[(1R)-3-{[(2R,3S,4R,7S,8S,11S,13R,16E)-17-ethyl-4,8-dihydroxy-3,7,11,13-tetramethyl-6,15-dioxononadeca-16,18-dien-2-yl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid (BKM)
Ligand formula: C33 H52 O11
Ligand molecular weight: 624.759
Ligand SMILES: CCC(=CC(=O)CC(C)CC(C)CCC(C(C)C(=O)CC(C(C)C(C)OC(=O)CC(C(=C(C)C(=O)O)C(=O)O)O)O)O)C=C
Ligand InChI: InChI=1S/C33H52O11/c1-9-24(10-2)15-25(34)14-19(4)13-18(3)11-12-26(35)21(6)28(37)16-27(36)20(5)23(8)44-30(39)17-29(38)31(33(42)43)22(7)32(40)41/h9,15,18-21,23,26-27,29,35-36,38H,1,10-14,16-17H2,2-8H3,(H,40,41)(H,42,43)/b24-15-,31-22-/t18-,19+,20+,21-,23+,26-,27+,29+/m0/s1
Release date: 2017-11-29
Crystal Structure Analysis of human PRPK complex with a compound (PDB entry 7SZC)
Macromolecule: EKC/KEOPS complex subunit TP53RK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6
Sequence length: 255 residues
Sequence: GPMAAARATTPADGEEPAPEAEALAAARERSSRFLSGLELVKQGAEARVFRGRFQGRAAVIKHRFPKGYRHPALEARLGRRRTVQEARALLRCRRAGISAPVVFFVDYASNCLYMEEIEGSVTVRDYIQSTMETEKTPQGLSNLAKTIGQVLARMHDEDLIHGDLTTSNMLLKPPLEQLNIVLIDFGLSFISALPEDKGVDLYVLEKAFLSTHPNTETVFEAFLKSYSTSSKKARPVLKKLDEVRLRGRKRSMVG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1772
R free: 0.2071
Average B factor: 37.0314
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 200mM Potassium sodium tartrate
Matthews coefficient: 2.34
Solvent content (%): 47.38
Ligand: D(-)-TARTARIC ACID (TAR)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m0/s1
Release date: 2022-12-14
TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH 6-[4-(3-CHLORO-4-FLUOROPHENYL)-1-(2-HYDROXYETHYL)-1H-IMIDAZOL-5-YL]IMIDAZO[1,2-B]PYRIDAZINE-3-CARBONITRILE (PDB entry 5QU0)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 307 residues
Sequence: GHMTIARDIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.177
R free: 0.206
Average B factor: 22.48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 23%(w/v) PEG3350, 3%(v/v) glcyerol
Matthews coefficient: 2.1
Solvent content (%): 41.33
Ligand: 6-[4-(3-chloro-4-fluorophenyl)-1-(2-hydroxyethyl)-1H-imidazol-5-yl]imidazo[1,2-b]pyridazine-3-carbonitrile (QMV)
Ligand formula: C18 H12 Cl F N6 O
Ligand molecular weight: 382.779
Ligand SMILES: c1cc(c(cc1c2c(n(cn2)CCO)c3ccc4ncc(n4n3)C#N)Cl)F
Ligand InChI: InChI=1S/C18H12ClFN6O/c19-13-7-11(1-2-14(13)20)17-18(25(5-6-27)10-23-17)15-3-4-16-22-9-12(8-21)26(16)24-15/h1-4,7,9-10,27H,5-6H2
Release date: 2020-02-05
Crystal Structure of D181A hFen1 in complex with DNA (PDB entry 5ZOE)
Macromolecule: Flap endonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 333 residues
Sequence: MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMACLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.215
R free: 0.2271
Average B factor: 47.5106
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: PEG 3350, MgCl2, Tris, KCl
Matthews coefficient: 2.33
Solvent content (%): 47.21
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2019-01-30
GTB mutant without mercury - E303C (PDB entry 5CQN)
Macromolecule: Histo-blood group ABO system transferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.40
Sequence length: 294 residues
Sequence: FMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVGAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPSFYGSSREAFTYERRPQSQAYIPKDEGDFYYMGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDCSHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPKNHQAVRNPE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.1839
R free: 0.2065
Average B factor: 25.467
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) MPD, 0.32 M ammonium sulfate, 0.25 M NaCl, and 0.2 M ADA pH 7.5
Matthews coefficient: 2.25
Solvent content (%): 45.29
Release date: 2016-10-26
Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor (PDB entry 6DD4)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.19463
R free: 0.22555
Average B factor: 44.064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 27.5% PEG3350, 200 mM LiSO4, 0.1M SBG, pH 7.0
Matthews coefficient: 2.57
Solvent content (%): 52.1
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2018-05-23
Crystal structure of APT1 bound to 2-Bromopalmitate (PDB entry 6QGN)
Macromolecule: Acyl-protein thioesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 233 residues
Sequence: GSRMSGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.099
R work: 0.23
R free: 0.2733
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: D1 Morpheus (Molecular Dimensions)
0.1 M  imidazole, 0.1 M MES monohydrate, 20% v/v PEG 500 MME, 10% w/v PEG 2000, 20 mM  1,6-Hexanediol,  20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2- Propanol, 20 mM 1,4-Butanediol, 20 mM 1,3-Propanediol, pH 6.5.
Matthews coefficient: 2.82
Solvent content (%): 56.42
Ligand: 2-Bromopalmitic acid (J1W)
Ligand formula: C16 H31 Br O2
Ligand molecular weight: 335.32
Ligand SMILES: CCCCCCCCCCCCCCC(C(=O)O)Br
Ligand InChI: InChI=1S/C16H31BrO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15(17)16(18)19/h15H,2-14H2,1H3,(H,18,19)/t15-/m1/s1
Release date: 2020-02-05
HsMetAP (F220M) in complex with 1-amino-2-propylpentyl]phosphonic acid (PDB entry 4U6W)
Macromolecule: Methionine aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 306 residues
Sequence: YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLMHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMSQF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.176
R free: 0.224
Average B factor: 30.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 15% PEG-MME, 100mM Hepes, PH 6
Matthews coefficient: 2.51
Solvent content (%): 50.91
Ligand: COBALT (II) ION (CO)
Ligand formula: Co
Ligand molecular weight: 58.933
Ligand SMILES: [Co+2]
Ligand InChI: InChI=1S/Co/q+2
Release date: 2015-03-25
The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-3,5-dichloro-N-methylphenylsulfonimidoyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 8CHQ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.01
R work: 0.149
R free: 0.1661
Average B factor: 11.947
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG3350, 0.2 M ammonium acetate, 0.1M HEPES-NaOH pH 7.5
Matthews coefficient: 2.34
Solvent content (%): 47.45
Ligand: (1S,5S,6R)-10-[S-[3,5-bis(chloranyl)phenyl]-N-methyl-sulfonimidoyl]-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (UMR)
Ligand formula: C23 H26 Cl2 N4 O2 S
Ligand molecular weight: 493.449
Ligand SMILES: CN=S(=O)(c1cc(cc(c1)Cl)Cl)N2C3CCCC2C(=O)N(CC3C=C)Cc4ccccn4
Ligand InChI: InChI=1S/C23H26Cl2N4O2S/c1-3-16-14-28(15-19-7-4-5-10-27-19)23(30)22-9-6-8-21(16)29(22)32(31,26-2)20-12-17(24)11-18(25)13-20/h3-5,7,10-13,16,21-22H,1,6,8-9,14-15H2,2H3/t16-,21+,22-,32-/m0/s1
Release date: 2023-09-06