satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000531a (PDB entry 5QFI)
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): 1.68
R work: 0.189
R free: 0.2183
Average B factor: 39.3681
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: 3.31
Solvent content (%): 62.79
Ligand: (1R,4R,5R,6S)-4,6-dihydroxy-N-phenyl-2-azabicyclo[3.3.1]nonane-2-carboxamide (JOG)
Ligand formula: C15 H20 N2 O3
Ligand molecular weight: 276.331
Ligand SMILES: c1ccc(cc1)NC(=O)N2CC(C3CC2CCC3O)O
Ligand InChI: InChI=1S/C15H20N2O3/c18-13-7-6-11-8-12(13)14(19)9-17(11)15(20)16-10-4-2-1-3-5-10/h1-5,11-14,18-19H,6-9H2,(H,16,20)/t11-,12-,13+,14+/m1/s1
Release date: 2018-10-10
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000519b (PDB entry 7GSN)
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): 1.87
R work: 0.1884
R free: 0.2289
Average B factor: 40.398
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: 3.32
Solvent content (%): 62.97
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
Structure of a semisynthetic phosphorylated DAPK (PDB entry 4UV0)
Macromolecule: DEATH-ASSOCIATED PROTEIN KINASE 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 323 residues
Sequence: GPMTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSRKACAVNMEKFKKFAARKKWKQSVRLISLCQRLSRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.1931
R free: 0.2425
Crystal growth procedure: 5MM HEPES, 30 MM NACL, 10 MM NA2SO4,0.5 MMDTT,25% (W/V) PEGMME2000
Matthews coefficient: 3.1
Solvent content (%): 60
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2015-08-12
Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives (PDB entry 6L12)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 289 residues
Sequence: GPHMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1968
R free: 0.2098
Average B factor: 39.683
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 0.4M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 3.58
Solvent content (%): 65.67
Ligand: 4-[(2-chloranylphenoxazin-10-yl)methyl]cyclohexan-1-amine (E2R)
Ligand formula: C19 H21 Cl N2 O
Ligand molecular weight: 328.836
Ligand SMILES: c1ccc2c(c1)N(c3cc(ccc3O2)Cl)CC4CCC(CC4)N
Ligand InChI: InChI=1S/C19H21ClN2O/c20-14-7-10-19-17(11-14)22(12-13-5-8-15(21)9-6-13)16-3-1-2-4-18(16)23-19/h1-4,7,10-11,13,15H,5-6,8-9,12,21H2/t13-,15-
Release date: 2020-05-27
ATP-dependent RNA helicase DDX39A (URH49delta41) (PDB entry 8IJU)
Macromolecule: ATP-dependent RNA helicase DDX39A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 396 residues
Sequence: GPLGSPGIPMHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVNGQVTVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLSIKKDEEVLKKNCPHVVVGTPGRILALVRNRSFSLKNVKHFVLDECDKMLEQLDMRRDVQEIFRLTPHEKQCMMFSATLSKDIRPVCRKFMQDPMEVFVDDETKLTLHGLQQYYVKLKDSEKNRKLFDLLDVLEFNQVIIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNVAELPEEIDISTYIEQSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1843
R free: 0.2219
Average B factor: 32.51
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 mM Na2PO4, 30 % (w/v) PEG3350
Matthews coefficient: 2.32
Solvent content (%): 47.1
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2024-01-24
Crystal structure of ternary complex of Pol theta polymerase domain (PDB entry 7ZUS)
Macromolecule: DNA polymerase theta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 726 residues
Sequence: SSSESLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRSLTSSKTATIGSRFKQASSPQEIPIRDDGFPIKGCDDTLVVGLAVCWGGRDAYYFSLQKEQKHSEISASLVPPSLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGMETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPNREMKNQGSKKTLGSTRRGIDNGRKLRLGRQFSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQNVPRDFEIKMGGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLETFHSTFKSHGHREGMLQSDQTGLSRKRKLQGMFCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELKDFDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.2008
R free: 0.2384
Average B factor: 71.064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.9
Crystallization temperature (K): 285
Crystal growth procedure: 15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate.
Matthews coefficient: 2.7
Solvent content (%): 54.4
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-10-12
Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- Methylmorpholin-4-yl)-1-(3-methyl-2-oxo- butyl)-2-(trifluoromethyl)-3, 4-dihydro-2H-pyrimido(1,2-a)pyrimidin-6- one, processed with the CrystalDirect automated mounting and cryo-cooling technology (PDB entry 5ANL)
Macromolecule: PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.137
Sequence length: 601 residues
Sequence: GAMSDHDLKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.20534
R free: 0.26667
Average B factor: 45.423
Crystal growth procedure: 0.1 M TRIS, PH=7.5, 1.8 M AMMONIUM SULFATE
Matthews coefficient: 2.88
Solvent content (%): 57.3
Ligand: (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one (RBQ)
Ligand formula: C17 H25 F3 N4 O3
Ligand molecular weight: 390.401
Ligand SMILES: CC(C)OCCN1C(CCN2C1=NC(=CC2=O)N3CCOCC3)C(F)(F)F
Ligand InChI: InChI=1S/C17H25F3N4O3/c1-12(2)27-10-7-23-13(17(18,19)20)3-4-24-15(25)11-14(21-16(23)24)22-5-8-26-9-6-22/h11-13H,3-10H2,1-2H3/t13-/m0/s1
Release date: 2016-04-13
APE1 exonuclease substrate complex with a C/T mismatch (PDB entry 5WN4)
Macromolecule: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: TCGACGGATCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.204
R free: 0.249
Average B factor: 51.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.61
Solvent content (%): 52.8
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-02-28
Crystal structure of Ser/Thr kinase Pim1 in complex with Mitoxantrone derivatives (PDB entry 4RBL)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 289 residues
Sequence: GPHMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.18837
R free: 0.24866
Average B factor: 64.217
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.4 M potassium sodium, tartrate tetrahydrate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 3.37
Solvent content (%): 63.53
Ligand: 1,4,5,8-tetrahydroxyanthracene-9,10-dione (3O7)
Ligand formula: C14 H8 O6
Ligand molecular weight: 272.21
Ligand SMILES: c1cc(c2c(c1O)C(=O)c3c(ccc(c3C2=O)O)O)O
Ligand InChI: InChI=1S/C14H8O6/c15-5-1-2-6(16)10-9(5)13(19)11-7(17)3-4-8(18)12(11)14(10)20/h1-4,15-18H
Release date: 2015-03-18
Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin (PDB entry 7M4O)
Macromolecule: E3 ubiquitin-protein ligase RNF216
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 138 residues
Sequence: GPEELAEKDDIKYRTSIEEKMTAARIRKCHKCGTGLIKSEGANRMSCRCGAQMCYLCRVSINGYDHFCQHPRSPGAPCQECSRCSLWTDPTEDDEKLIEEIQKEAEEEQKRKNGENTFKRIGPPLEKPVEKVQRVEAL
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.2008
R free: 0.2519
Average B factor: 41.76
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.22
Crystallization temperature (K): 293
Crystal growth procedure: 0.259 M ammonium sulfate, 30.1 % PEG monomethyl ether 2000, 0.1M sodium acetate-acetic acid pH 5.22
Matthews coefficient: 2.39
Solvent content (%): 48.46
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: 2022-01-05
Crystal Structure of Human NEIL1(P2G) bound to duplex DNA containing Thymine Glycol (PDB entry 5ITY)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 400 residues
Sequence: MGEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKSKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRRKGRQAASGHCRPRKVKADIPSLEPEGTSASAALGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.17552
R free: 0.22456
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M cacodylic acid (pH 7.0), 0.1M NaCl, 0.05M MgCl2, 24%(w/v) PEG 8000
Matthews coefficient: 2.19
Solvent content (%): 43.84
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2016-07-06
HIGH-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA/CSKN2A1 GENE PRODUCT) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR THN27 (PDB entry 6HBN)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.187
R free: 0.2172
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 90 MIKROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER INHIBITOR STOCK SOLUTION (10 MM INHIBITOR IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 4.4 M NACL, 0.1 M CITRIC ACID, PH 5.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/INHIBITOR MIXTURE.,VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K
Matthews coefficient: 2.06
Solvent content (%): 40.35
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: 2019-03-27
Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ (PDB entry 6KHS)
Macromolecule: Methyltransferase N6AMT1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 214 residues
Sequence: MAGENFATPFHGHVGRGAFSDVYEPAEDTFLLLDALEAAAAELAGVEICLEVGSGSGVVSAFLASMIGPQALYMCTDINPEAAACTLETARCNKVHIQPVITDLVKGLLPRLTEKVDLLVFNPPYVVTPPQEVGSHGIEAAWAGGRNGREVMDRFFPLVPDLLSPRGLFYLVTIKENNPEEILKIMKTKGLQGTTALSRQAGQETLSVLKFTKS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.895
R work: 0.1874
R free: 0.2198
Average B factor: 25.0376
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.26 Msodium phosphate monobasic monohydrate 
0.14 Mpotassium phosphate dibasic 
pH 5.6
Matthews coefficient: 3.28
Solvent content (%): 62.45
Ligand: N5-METHYLGLUTAMINE (MEQ)
Ligand formula: C6 H12 N2 O3
Ligand molecular weight: 160.171
Ligand SMILES: CNC(=O)CCC(C(=O)O)N
Ligand InChI: InChI=1S/C6H12N2O3/c1-8-5(9)3-2-4(7)6(10)11/h4H,2-3,7H2,1H3,(H,8,9)(H,10,11)/t4-/m0/s1
Release date: 2020-07-15
Crystal structure of the KAT6A WH domain and its bound double stranded DNA (PDB entry 7Y43)
Macromolecule: Histone acetyltransferase KAT6A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 86 residues
Sequence: SMVKLANPLYTEWILEAIKKVKKQKQRPSEERICNAVSSSHGLDRKTVLEQLELSVKDGTILKVSNKGLNSYKDPDNPGRIALPKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2269
R free: 0.2352
Average B factor: 34.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M magnesium acetate tetrahydrate, 20% polyethylene glycol 3,350
Matthews coefficient: 2.27
Solvent content (%): 45.93
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2023-01-18
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13706a (PDB entry 5R5H)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1844
R free: 0.2298
Average B factor: 30.043
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2
Solvent content (%): 38.64
Ligand: 3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide (JOV)
Ligand formula: C11 H14 Cl N O2
Ligand molecular weight: 227.687
Ligand SMILES: CC(C)(CO)NC(=O)c1cccc(c1)Cl
Ligand InChI: InChI=1S/C11H14ClNO2/c1-11(2,7-14)13-10(15)8-4-3-5-9(12)6-8/h3-6,14H,7H2,1-2H3,(H,13,15)
Release date: 2020-07-01
Crystal structure of mouse PRMT6 with modified H7-4 peptide (PDB entry 6SQK)
Macromolecule: Protein arginine N-methyltransferase 6
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.1.1.319
Sequence length: 380 residues
Sequence: GHMSLSKKRKLESGDSGGAGAGGEGAEEENGGEQEAAPPRPRRTKSERDQLYYECYSDVSVHEEMIADQVRTEAYRLGILKNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRLNGLEDRVHVLPGPVETVELPERVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFVAPISDQMLEWRLGFWSQVKQHYGVDMSCMESFATRCLMGHSEIVVQDLSGEDVLARPQRFAQLELARAGLEQELEAGVGGRFRCSCYGSAPLHGFAVWFQVTFPGGDSEKPLVLSTSPLHPATHWKQALLYLNEPVPVEQDTDISGEITLLPSPDNPRRLRILLRYKVGDHEEKTKDFAMED
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.19
R free: 0.2128
Average B factor: 27.3722
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3,350 20%, Mg(CH3COO)2 200 mM, HEPES-NaOH pH 7.0 100 mM
Matthews coefficient: 2.3
Solvent content (%): 46.55
Release date: 2020-09-30
Crystal structure of the human RAD9-HUS1-RAD1-RHINO complex (PDB entry 6J8Y)
Macromolecule: Cell cycle checkpoint control protein RAD9A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.11.2
Sequence length: 270 residues
Sequence: MKCLVTGGNVKVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDLLRCKILMKSFLSVFRSLAMLEKTVEKCCISLNGRSSRLVVQLHCKFGVRKTHNLSFQDCESLQAVFDPASCPHMLRAPARVLGEAVLPFSPALAEVTLGIGRGRRVILRSYHEEEADSTAKAMVTEMCLGEEDFQQLQAQEGVAITFCLKEFRGLLSFAESANLNLSIHFDAPGRPAIFTIKDSLLDGHFVLATLSDTDS
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2184
R free: 0.2581
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, Sodium citrate, Bis-tris propane pH 7.5
Matthews coefficient: 2.88
Solvent content (%): 57.31
Release date: 2019-12-04
Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor 3a (PDB entry 6MA4)
Macromolecule: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.255
Sequence length: 723 residues
Sequence: GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIKPVE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1908
R free: 0.2204
Average B factor: 34.6358
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 1.05 M Sodium Citrate Tribasic Dihydrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 3.1
Solvent content (%): 60.38
Ligand: 5-{2-[(1R)-2-{(carboxymethyl)[(thiophen-2-yl)methyl]amino}-2-oxo-1-{[(2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}ethyl]phenoxy}pentanoic acid (JA7)
Ligand formula: C29 H29 N3 O9 S2
Ligand molecular weight: 627.685
Ligand SMILES: c1ccc(c(c1)C(C(=O)N(Cc2cccs2)CC(=O)O)NS(=O)(=O)c3ccc4c(c3)C=CC(=O)N4)OCCCCC(=O)O
Ligand InChI: InChI=1S/C29H29N3O9S2/c33-25-13-10-19-16-21(11-12-23(19)30-25)43(39,40)31-28(29(38)32(18-27(36)37)17-20-6-5-15-42-20)22-7-1-2-8-24(22)41-14-4-3-9-26(34)35/h1-2,5-8,10-13,15-16,28,31H,3-4,9,14,17-18H2,(H,30,33)(H,34,35)(H,36,37)/t28-/m1/s1
Release date: 2018-10-17