satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human galactokinase 1 bound with N-(Cyclobutylmethyl)-1,5-dimethyl-1H-pyrazole-4-carboxamide (PDB entry 6Q8Z)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 392 residues
Sequence: HAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGKESLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2409
R free: 0.2834
Average B factor: 47.0671
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MOPS/sodium HEPES pH7-7.5, 40-50% Morpheus precipitant mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1M Morpheus carboxylic acids mix (0.02M each of: sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium oxamate and potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.95
Solvent content (%): 58.37
Ligand: beta-D-galactopyranose (GAL)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6-/m1/s1
Release date: 2019-01-23
Crystal structure of SMYD3 with SAM and EPZ030456 (PDB entry 5CCM)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 428 residues
Sequence: MEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2005
R free: 0.2551
Average B factor: 34.062
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350
Matthews coefficient: 2.2
Solvent content (%): 44.11
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: 2015-09-09
Crystal structure of CK2 (PDB entry 5KU8)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 331 residues
Sequence: SGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.183
R free: 0.216
Average B factor: 35.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 22-26% PEG 6K, 200 mM ammonium sulfate, 100 mM MES
Matthews coefficient: 3.12
Solvent content (%): 60.56
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: 2017-11-08
Hypoxia-Inducible Factor (HIF) Prolyl Hydroxylase 2 (PHD2) in Complex with the Carboxamide Analog JNJ43058171 (PDB entry 6NMQ)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 213 residues
Sequence: RPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.22247
R free: 0.25986
Average B factor: 17.556
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2M AMMONIUM SULFATE/100MM IMIDAZOLE, 100 MM MAGNESIUM SULFATE/10% (V/V) GLYCEROL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 3.2
Solvent content (%): 61.56
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2019-04-24
Crystal Structure of human cyclic GMP-AMP synthase (PDB entry 7FU7)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.2227
R free: 0.2463
Average B factor: 98.7999
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals
Matthews coefficient: 2.56
Solvent content (%): 51.92
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: 2024-02-21
GTPase HRAS mutant D33K under 900 MPa pressure (PDB entry 7OGF)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYKPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.242
R free: 0.333
Average B factor: 19.27
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 40 mM Tris HCL, 10 mM MgCl2, 2 mM DTE, 26-30 % PEG-400
Matthews coefficient: 1.87
Solvent content (%): 34.11
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2022-02-09
Substrate Free Cytochrome P450 3A5 (CYP3A5) (PDB entry 6MJM)
Macromolecule: Cytochrome P450 3A5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.1
Sequence length: 480 residues
Sequence: MALYGTRTHGLFKRLGIPGPTPLPLLGNVLSYRQGLWKFDTECYKKYGKMWGTYEGQLPVLAITDPDVIRTVLVKECYSVFTNRRSLGPVGFMKSAISLAEDEEWKRIRSLLSPTFTSGKLKEMFPIIAQYGDVLVRNLRREAEKGKPVTLKDIFGAYSMDVITGTSFGVNIDSLNNPQDPFVESTKKFLKFGFLDPLFLSIILFPFLTPVFEALNVSLFPKDTINFLSKSVNRMKKSRLNDKQKHRLDFLQLMIDSQNSKETESHKALSDLELAAQSIIFIFAGYETTSSVLSFTLYELATHPDVQQKLQKEIDAVLPNKAPPTYDAVVQMEYLDMVVNETLRLFPVAIRLERTCKKDVEINGVFIPKGSMVVIPTYALHHDPKYWTEPEEFRPERFSKKKDSIDPYIYTPFGTGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLDTQGLLQPEKPIVLKVDSRDGHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2092
R free: 0.248
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 297
Crystal growth procedure: PEG 3350, ADA, Anapoe 20
Matthews coefficient: 2.36
Solvent content (%): 47.91
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2019-04-03
Crystal structure of human SHIP2 catalytic domain (PDB entry 6SRR)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 316 residues
Sequence: SMDEPDMISVFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDREWLDLLRGGLKELTDLDYRPIAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGNKGAVGVSFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRLLSLGDRQLNAFDISLRFTHLFWFGDLNYRLDMDIQEILNYISRKEFEPLLRVDQLNLEREKHKVFLRFSEEEISFPPTYRYERGSRDTYAWHKQKPTGVRTNVPSWCDRILWKSYPETHIICNSYGCTDDIVTSDHSPVFGTFEVGVTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1865
R free: 0.2371
Average B factor: 80.2604
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M Sodium citrate, 20 % w/v PEG 3000
Matthews coefficient: 2.28
Solvent content (%): 45.98
Release date: 2021-01-13
Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 8 (CS275) (PDB entry 6T6F)
Macromolecule: Calcium/calmodulin-dependent protein kinase type 1D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 322 residues
Sequence: SMSSWKKQAEDIKKIFEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKALKGKESSIENEIAVLRKIKHENIVALEDIYESPNHLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIMISDFGLSKMEGKGDVMSTACGTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLFEQILKAEYEFDSPYWDDISDSAKDFIRNLMEKDPNKRYTCEQAARHPWIAGDTALNKNIHESVSAQIRKNFAKSKWRQAFNATAVVRHMRKLHLGSSLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.2099
R free: 0.2376
Average B factor: 53.7188
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 28% PEG3350 -- 0.1M bis-tris pH 5.5 -- 0.2M ammonium acetate
Matthews coefficient: 2.34
Solvent content (%): 47.41
Ligand: 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3-(trifluoromethyl)phenyl]amino]pyrimidine-5-carboxamide (MMW)
Ligand formula: C17 H19 F3 N6 O
Ligand molecular weight: 380.368
Ligand SMILES: c1cc(cc(c1)Nc2c(cnc(n2)N3CCCC(C3)N)C(=O)N)C(F)(F)F
Ligand InChI: InChI=1S/C17H19F3N6O/c18-17(19,20)10-3-1-5-12(7-10)24-15-13(14(22)27)8-23-16(25-15)26-6-2-4-11(21)9-26/h1,3,5,7-8,11H,2,4,6,9,21H2,(H2,22,27)(H,23,24,25)/t11-/m0/s1
Release date: 2020-01-15
Crystal structure of human NEIL1(K242) bound to duplex DNA containing a cleaved C:T mismatch (PDB entry 6LWR)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2084
R free: 0.2477
Average B factor: 92.059
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.78
Solvent content (%): 55.7
Release date: 2021-06-09
BACE crystal structure with hydroxy pyrrolidine inhibitor (PDB entry 6BFE)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.173
R free: 0.2
Average B factor: 18.26
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 276
Crystal growth procedure: 17% PEG 8000, 0.2M ammonium sulfate, 0.1% cacodylate, pH 7.4
Matthews coefficient: 2.58
Solvent content (%): 52.32
Ligand: N-[(1R,2S)-1-[(2R,4R)-4-(cyclohexylmethoxy)pyrrolidin-2-yl]-3-(3,5-difluorophenyl)-1-hydroxypropan-2-yl]acetamide (DJV)
Ligand formula: C22 H32 F2 N2 O3
Ligand molecular weight: 410.498
Ligand SMILES: CC(=O)NC(Cc1cc(cc(c1)F)F)C(C2CC(CN2)OCC3CCCCC3)O
Ligand InChI: InChI=1S/C22H32F2N2O3/c1-14(27)26-21(9-16-7-17(23)10-18(24)8-16)22(28)20-11-19(12-25-20)29-13-15-5-3-2-4-6-15/h7-8,10,15,19-22,25,28H,2-6,9,11-13H2,1H3,(H,26,27)/t19-,20-,21+,22-/m1/s1
Release date: 2017-11-15
Heterodimers of FALS mutant SOD enzyme (PDB entry 6DTK)
Macromolecule: Superoxide dismutase C111S/D83S-C111S HETERODIMER
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.15.1.1
Sequence length: 323 residues
Sequence: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGSLGNVTADKDGVADVSIEDSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQGAAASGGGGGSGGGGSATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGSLGNVTADKDGVADVSIEDSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.156
R free: 0.19
Average B factor: 38.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2-3 M Ammonium sulfate or Sodium malonate
Matthews coefficient: 3.65
Solvent content (%): 66.27
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: 2019-06-19
E. coli Microcin-processing metalloprotease TldD/E with angiotensin analogue bound (PDB entry 5NJA)
Macromolecule: Metalloprotease TldD
Type: Protein, polypeptide(L)
Source organism: Escherichia coli str. K-12 substr. MG1655
EC number: 3.4
Sequence length: 495 residues
Sequence: MGSSHHHHHHSQDPMSLNLVSEQLLAANGLKHQDLFAILGQLAERRLDYGDLYFQSSYHESWVLEDRIIKDGSYNIDQGVGVRAISGEKTGFAYADQISLLALEQSAQAARTIVRDSGDGKVQTLGAVEHSPLYTSVDPLQSMSREEKLDILRRVDKVAREADKRVQEVTASLSGVYELILVAATDGTLAADVRPLVRLSVSVLVEEDGKRERGASGGGGRFGYEFFLADLDGEVRADAWAKEAVRMALVNLSAVAAPAGTMPVVLGAGWPGVLLHEAVGHGLEGDFNRRGTSVFSGQVGELVASELCTVVDDGTMVDRRGSVAIDDEGTPGQYNVLIENGILKGYMQDKLNARLMGMTPTGNGRRESYAHLPMPRMTNTYMLPGKSTPQEIIESVEYGIYAPNFGGGQVDITSDKFVFSTSEAYLIENGKVTKPVKGATLIGSGIETMQQISMVGNDLKLDNGVGVCGKEGQSLPVGVGQPTLKVDNLTVGGTA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1303
R free: 0.1712
Average B factor: 16.345
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Matthews coefficient: 2.29
Solvent content (%): 46.17
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: 2017-10-04
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000608a (PDB entry 5QE6)
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): 1.774
R work: 0.1954
R free: 0.2117
Average B factor: 42.7408
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.29
Solvent content (%): 62.66
Ligand: 3-chloro-4-(4-methylpiperidin-1-yl)aniline (JHA)
Ligand formula: C12 H17 Cl N2
Ligand molecular weight: 224.73
Ligand SMILES: CC1CCN(CC1)c2ccc(cc2Cl)N
Ligand InChI: InChI=1S/C12H17ClN2/c1-9-4-6-15(7-5-9)12-3-2-10(14)8-11(12)13/h2-3,8-9H,4-7,14H2,1H3
Release date: 2018-10-10
Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 (PDB entry 7Q40)
Macromolecule: E3 ubiquitin-protein ligase HERC2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 405 residues
Sequence: GAMGSLIRKKAAGLESAATIRTKVFVWGLNDKDQLGGLKGSKIKVPSFSETLSALNVVQVAGGSKSLFAVTVEGKVYACGEATNGRLGLGISSGTVPIPRQITALSSYVVKKVAVHSGGRHATALTVDGKVFSWGEGDDGKLGHFSRMNCDKPRLIEALKTKRIRDIACGSSHSAALTSSGELYTWGLGEYGRLGHGDNTTQLKPKMVKVLLGHRVIQVACGSRDAQTLALTDEGLVFSWGDGDFGKLGRGGSEGCNIPQNIERLNGQGVCQIECGAQFSLALTKSGVVWTWGKGDYFRLGHGSDVHVRKPQVVEGLRGKKIVHVAVGALHCLAVTDSGQVYAWGDNDHGQQGNGTTTVNRKPTLVQGLEGQKITRVACGSSHSVAWTTVDVATPSVHEPVLFQT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35002226075
R work: 0.178924037543
R free: 0.230322144529
Average B factor: 56.9293356942
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: hanging drop
20% PEG 3350
0.18M tris amonium citrate
Matthews coefficient: 3.05
Solvent content (%): 59.73
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2022-11-16
Human DNA polymerase eta-DNA ternary complex: reaction with 1 mM Mn2+ for 180s (PDB entry 5KFC)
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): 1.5
R work: 0.1802
R free: 0.2098
Average B factor: 21.9741
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.08
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2016-06-22
Crystal structure of Tandem Tudor Domain of human UHRF1 (PDB entry 5YYA)
Macromolecule: E3 ubiquitin-protein ligase UHRF1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 164 residues
Sequence: SDEDMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1719
R free: 0.2055
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 6.5), 200 mM ammonium acetate, 25% (w/v) polyethylene glycol (PEG) 3350
Matthews coefficient: 2.09
Solvent content (%): 41.06
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: 2018-12-12
Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant) (PDB entry 6RFK)
Macromolecule: Coagulation factor IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.22
Sequence length: 62 residues
Sequence: MDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.12607
R free: 0.16314
Average B factor: 33.236
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 297
Crystal growth procedure: 0.1M BIS-TRIS propane pH 8.5, 24% PEG 3350, 0.275M Na Malonate
Matthews coefficient: 3.42
Solvent content (%): 64
Ligand: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (B3P)
Ligand formula: C11 H26 N2 O6
Ligand molecular weight: 282.334
Ligand SMILES: C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
Ligand InChI: InChI=1S/C11H26N2O6/c14-4-10(5-15,6-16)12-2-1-3-13-11(7-17,8-18)9-19/h12-19H,1-9H2
Release date: 2019-06-12
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with CIT, Mg and ATP binding at allosteric site and Mg, ATP binding at active site. (PDB entry 6L59)
Macromolecule: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.41
Sequence length: 342 residues
Sequence: MGSTGGVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWMIPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKDLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.254
R work: 0.2003
R free: 0.2265
Average B factor: 50.6838
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 299
Crystal growth procedure: 0.2 M sodium citrate, pH 5.5, and 24% (v/v) PEG400
Matthews coefficient: 3.46
Solvent content (%): 64.46
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2020-04-29