satarupa22/MacromolecularLigandDB huggingface dataset:
Bivalent Inhibitor UNC4512 Bound to the TAF1 Bromodomain Tandem (PDB entry 6FIC)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 280 residues
Sequence: GTTVHCDYLNRPHKSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLDPMT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.20148
R free: 0.23595
Average B factor: 40.443
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 7.5, 4.2 M NaCl
Matthews coefficient: 4.13
Solvent content (%): 70.23
Ligand: 3-azanyl-2-[3-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[2-[[3-azanyl-1-[[2-[[3-methyl-6-[4-methyl-3-(methylsulfonyl-$l^{2}-azanyl)cyclohexa-1,3,5-trien-1-yl]-[1,2,4]triazolo[4,3-b]pyridazin-8-yl]-$l^{2}-azanyl]-2-oxidanylidene-ethyl]amino]-1-oxidanylidene-propan-2-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propanoylamino]-~{N}-[3-[[3-methyl-6-[4-methyl-3-(methylsulfonylamino)phenyl]-[1,2,4]triazolo[4,3-b]pyridazin-8-yl]amino]-3-oxidanylidene-propyl]propanamide (DKH)
Ligand formula: C76 H105 N18 O27 S2
Ligand molecular weight: 1766.881
Ligand SMILES: Cc1ccc(cc1NS(=O)(=O)C)c2cc(c3nnc(n3n2)C)NC(=O)CCNC(=O)C(CN)NC(=O)CCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCC(=O)NC(CN)C(=O)NCC(=O)[N]c4[c]c(nn5c4nnc5[C])c6[c][c]c(c([c]6)[N]S(=O)(=O)[C])[C]([C])[C]
Ligand InChI: InChI=1S/C78H124N18O27S2/c1-56(2)62-11-10-61(49-66(62)94-125(7,105)106)65-51-68(76-90-88-59(5)96(76)92-65)84-73(99)54-82-78(102)70(53-80)86-74(100)55-123-47-46-122-45-44-121-43-42-120-41-40-119-39-38-118-37-36-117-35-34-116-33-32-115-31-30-114-29-28-113-27-26-112-25-24-111-23-22-110-21-20-109-19-18-108-17-16-107-15-13-72(98)85-69(52-79)77(101)81-14-12-71(97)83-67-50-64(91-95-58(4)87-89-75(67)95)60-9-8-57(3)63(48-60)93-124(6,103)104/h8-11,48-51,56,69-70,93-94H,12-47,52-55,79-80H2,1-7H3,(H,81,101)(H,82,102)(H,83,97)(H,84,99)(H,85,98)(H,86,100)
Release date: 2018-01-31
Crystal structure of Tyrosine-protein kinase receptor in complex with 2,4-dichloro-N-(3-methyl-1-phenyl-1H-pyrazol-5-yl)benzamide Inhibitor (PDB entry 6D1Y)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 320 residues
Sequence: GSTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1766
R free: 0.2244
Average B factor: 18.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: Well volume: 25.0 uL
Well Ingredients:
Buffer: 0.1 M (5.0 uL of stock 0.5 M) ADA (pH 6.50)
Salt: 3.0 M (9.375 uL of stock 8.0 M) lithium nitrate

Plate setup temperature: 13 C
Plate incubation temperature: 4 C

Drop volume from well: 0.1 uL
Drop protein volume: 0.1 uL

Protein Formulation Composition:
Protein: (5.0 mg/mL) (0.14 mM)
Compound:  (3.00 mM)
Matthews coefficient: 2.34
Solvent content (%): 47.33
Ligand: 2,4-dichloro-N-(3-methyl-1-phenyl-1H-pyrazol-5-yl)benzamide (FQJ)
Ligand formula: C17 H13 Cl2 N3 O
Ligand molecular weight: 346.211
Ligand SMILES: Cc1cc(n(n1)c2ccccc2)NC(=O)c3ccc(cc3Cl)Cl
Ligand InChI: InChI=1S/C17H13Cl2N3O/c1-11-9-16(22(21-11)13-5-3-2-4-6-13)20-17(23)14-8-7-12(18)10-15(14)19/h2-10H,1H3,(H,20,23)
Release date: 2018-05-02
Crystal structure of MYST acetyltransferase domain in complex with inhibitor 41 (PDB entry 6PDD)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 272 residues
Sequence: KYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1709
R free: 0.2119
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292
Crystal growth procedure: 27% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5
Matthews coefficient: 2.52
Solvent content (%): 51.14
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-04-01
PRMT5/MEP50 crystal structure with MTA and an achiral, class 1, non-atropisomeric inhibitor bound (PDB entry 7UOH)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1967
R free: 0.2321
Average B factor: 78.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 11 %w/v PEG 4K
0.1 M Na3 Cititrate 5 pH
0.05 M Na Acetate
Matthews coefficient: 2.9
Solvent content (%): 57.61
Ligand: (2M)-2-[(4M)-4-{4-(aminomethyl)-1-oxo-8-[(2R)-oxolan-2-yl]-1,2-dihydrophthalazin-6-yl}-1-methyl-1H-pyrazol-5-yl]-1-benzothiophene-3-carbonitrile (NXF)
Ligand formula: C26 H22 N6 O2 S
Ligand molecular weight: 482.557
Ligand SMILES: Cn1c(c(cn1)c2cc(c3c(c2)C(=NNC3=O)CN)C4CCCO4)c5c(c6ccccc6s5)C#N
Ligand InChI: InChI=1S/C26H22N6O2S/c1-32-24(25-18(11-27)15-5-2-3-7-22(15)35-25)19(13-29-32)14-9-16-20(12-28)30-31-26(33)23(16)17(10-14)21-6-4-8-34-21/h2-3,5,7,9-10,13,21H,4,6,8,12,28H2,1H3,(H,31,33)/t21-/m1/s1
Release date: 2022-08-17
DesGla-XaS195A Bound to Aptamer 11F7t (PDB entry 5VOE)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 233 residues
Sequence: IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDAGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.21291
R free: 0.24841
Average B factor: 57.368
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Bicine, 0.1 M Tris base, 0.1 M Carboxylic Acids, 10% PEG 20,000, 20% PEG 500 monomethyl ester
Matthews coefficient: 3.3
Solvent content (%): 62.73
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-06-20
Structure of METTL6 bound with SAM (PDB entry 7F1E)
Macromolecule: tRNA N(3)-methylcytidine methyltransferase METTL6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 286 residues
Sequence: GHMASLQRKGLQARILTSEEEEKLKRDQTLVSDFKQQKLEQEAQKNWDLFYKRNSTNFFKDRHWTTREFEELRSCREFEDQKLTMLEAGCGVGNCLFPLLEEDPNIFAYACDFSPRAIEYVKQNPLYDTERCKVFQCDLTKDDLLDHVPPESVDVVMLIFVLSAVHPDKMHLVLQNIYKVLKPGKSVLFRDYGLYDHAMLRFKASSKLGENFYVRQDGTRSYFFTDDFLAQLFMDTGYEEVVNEYVFRETVNKKEGLCVPRVFLQSKFLKPPKNPSPVVLGLDPKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.589
R work: 0.1908
R free: 0.2265
Average B factor: 51.4533
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Sodium acetate pH5.2,  2.0M sodium formate
Matthews coefficient: 3.37
Solvent content (%): 63.52
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2022-01-12
Human DNA polymerase beta crosslinked ternary complex 1 (PDB entry 7RBG)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1789
R free: 0.2225
Average B factor: 21.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Citrate pH 5.5, 18% PEG6000
Matthews coefficient: 2.36
Solvent content (%): 47.8
Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Release date: 2022-03-09
Crystal structure of PTP epsilon D2 domain (A455N/V457Y/E597D) (PDB entry 6D4F)
Macromolecule: Receptor-type tyrosine-protein phosphatase epsilon
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 279 residues
Sequence: GGGGLEEEFRKLTNVRIMKENMRTGNLPANMKKNRYIQIIPYDFNRVILSMKRGQEYTDYINASFIDGYRQKDYFIATQGPLAHTVEDFWRMIWEWKSHTIVMLTEVQEREQDKCYQYWPTEGSVTHGEITIEIKNDTLSEAISIRDFLVTLNQPQARQEEQVRVVRQFHFHGWPDIGIPAEGKGMIDLIAAVQKQQQQTGNHPITVHCSAGAGRTGTFIALSNILERVKAEGLLDVFQAVKSLRLQRPHMVQTLEQYEFCYKVVQDFIDIFSDYANFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.909
R work: 0.19
R free: 0.225
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M imidazole pH 8.0, 0.2 M calcium acetate hydrate, 20% (w/v) polyethylene glycol 1000
Matthews coefficient: 2.63
Solvent content (%): 53.32
Ligand: PENTAETHYLENE GLYCOL (1PE)
Ligand formula: C10 H22 O6
Ligand molecular weight: 238.278
Ligand SMILES: C(COCCOCCOCCOCCO)O
Ligand InChI: InChI=1S/C10H22O6/c11-1-3-13-5-7-15-9-10-16-8-6-14-4-2-12/h11-12H,1-10H2
Release date: 2018-10-17
Crystal Structure of human phosphodiesterase 10 in complex with 6H-imidazo[1,2-c]quinazolin-5-one (PDB entry 5SGE)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1816
R free: 0.2241
Average B factor: 47.904
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.63
Solvent content (%): 53.17
Ligand: (4R,10aP)-imidazo[1,2-c]quinazolin-5(6H)-one (IWS)
Ligand formula: C10 H7 N3 O
Ligand molecular weight: 185.182
Ligand SMILES: c1ccc2c(c1)-c3nccn3C(=O)N2
Ligand InChI: InChI=1S/C10H7N3O/c14-10-12-8-4-2-1-3-7(8)9-11-5-6-13(9)10/h1-6H,(H,12,14)
Release date: 2022-10-12
Crystal structure of cytochrome P450 3A4 bound to progesterone and citrate (PDB entry 5A1P)
Macromolecule: CYTOCHROME P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.13.157
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1908
R free: 0.2779
Crystallization pH: 6.4
Crystal growth procedure: 6% PEG 3350, 20 MM BIS-TRIS PROPANE PH 6.4, 12 MM AMMONIUM CITRATE, 5% GLYCEROL
Matthews coefficient: 2.26
Solvent content (%): 45.5
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: 2015-06-24
Crystal Structure of KDM4D with tetrazole ligand GF049 (PDB entry 6F5S)
Macromolecule: Lysine-specific demethylase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 342 residues
Sequence: METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1608
R free: 0.1832
Average B factor: 34.408
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350
Matthews coefficient: 2.61
Solvent content (%): 52.85
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: 2018-12-12
Structure of SARS-CoV-2 Beta variant spike receptor-binding domain complexed with human ACE2 (PDB entry 7EKG)
Macromolecule: Angiotensin-converting enzyme 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.23
Sequence length: 603 residues
Sequence: STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.63
R work: 0.2138
R free: 0.2484
Average B factor: 73.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES, pH 6.5, 12% w/v PEG 20000
Matthews coefficient: 3.33
Solvent content (%): 63.02
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2021-11-03
DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mg2+ (960 min) (PDB entry 6VF2)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1681
R free: 0.1926
Average B factor: 29.4835
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.44
Solvent content (%): 49.68
Ligand: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTT)
Ligand formula: C4 H10 O2 S2
Ligand molecular weight: 154.251
Ligand SMILES: C(C(C(CS)O)O)S
Ligand InChI: InChI=1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2/t3-,4-/m0/s1
Release date: 2021-09-01
Crystal structure of PTPN2 catalytic domain (PDB entry 7F5O)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 305 residues
Sequence: SNAMPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLSPAFD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1989
R free: 0.241
Average B factor: 19.305
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris Propane (pH-7.5), 0.2 M Sodium Iodide, 20% w/v PEG 3350, 10% v/v Ethylene glycol and 0.9 mM Mitoxantrone additive
Matthews coefficient: 2.31
Solvent content (%): 46.68
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2021-12-29
Lysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with BB-287 (PDB entry 6YW0)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 252 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELNKPSDSVGKDVF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1923
R free: 0.2208
Average B factor: 71.7747
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Sample: 18 mg/mL PHD2-Me + 1 mM FeSO4 + 2 mM compound; Reservoir: 1.7% polyethylene glycol 400, 15% glycerol, 1.7 M ammonium sulphate and 0.085 M HEPES-Na pH 7.5; Sitting drop (2 uL), protein-to-well ratio, 1:1
Matthews coefficient: 3.09
Solvent content (%): 60.25
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2020-12-30
Structure of CD148 fibronectin type III domain 2 (PDB entry 7U01)
Macromolecule: Receptor-type tyrosine-protein phosphatase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 159 residues
Sequence: EPIPVSDLRVALTGVRKAALSWSNGNGTASCRMLLESIGSHEELTQDSRLQVNISGLKPGVQYNINPYLLQSNKTKGDPLGTEGGLDASNTERSRAGSPTAPMHDESLVGPVDPSSGQQSRDTEVLLVGLEPGTRYNATVYSQAANGTEGQPQAIEFRT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29707910798
R work: 0.213740512015
R free: 0.260416175608
Average B factor: 69.786072096
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium acetate pH4.5, 3M NaCl
Matthews coefficient: 2.13
Solvent content (%): 42.29
Release date: 2023-02-22
ATAD2 in complex with FragLite7 (PDB entry 7QX1)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.2046
R free: 0.2424
Average B factor: 34.025
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
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: 2022-11-23