satarupa22/MacromolecularLigandDB huggingface dataset:
H-Ras Y137E (PDB entry 4XVQ)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSEGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.887
R work: 0.2025
R free: 0.2536
Average B factor: 29.64
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 152mM Ca(OAc)2, 24.8% PEG 3350, 4.8% stabilization buffer at pH 7.5.
Matthews coefficient: 1.88
Solvent content (%): 34.57
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: 2015-06-17
Crystal structure of human Biliverdin IX-beta reductase B (PDB entry 7ER6)
Macromolecule: Flavin reductase (NADPH)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.30
Sequence length: 206 residues
Sequence: MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQYQ
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1619
R free: 0.198
Average B factor: 23.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 1.9M-2.0M Ammonium sulfate, 0.1M Bis-tris (pH 6.5)
Matthews coefficient: 2.26
Solvent content (%): 45.46
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2022-01-19
Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine competitive inhibitor (PDB entry 5VAR)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 119 residues
Sequence: GSHMQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.194
R free: 0.243
Average B factor: 28.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 290
Crystal growth procedure: 18%(w/v) PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5
Matthews coefficient: 2.12
Solvent content (%): 42.08
Ligand: (1R,2S,3R,4S)-3-[(dimethylamino)methyl]-1-phenylbicyclo[2.2.1]heptan-2-ol (92Y)
Ligand formula: C16 H23 N O
Ligand molecular weight: 245.36
Ligand SMILES: CN(C)CC1C2CCC(C2)(C1O)c3ccccc3
Ligand InChI: InChI=1S/C16H23NO/c1-17(2)11-14-12-8-9-16(10-12,15(14)18)13-6-4-3-5-7-13/h3-7,12,14-15,18H,8-11H2,1-2H3/t12-,14-,15-,16+/m0/s1
Release date: 2018-03-28
Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing undamaged template dG and bound incoming CMPCPP (PDB entry 6P1W)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.751
R work: 0.1632
R free: 0.1899
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 82mM HEPES pH 7.5, 82mM NaCl, 8.2% w/v PEG4000
Matthews coefficient: 2.84
Solvent content (%): 56.7
Ligand: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine (2TM)
Ligand formula: C10 H18 N3 O13 P3
Ligand molecular weight: 481.184
Ligand SMILES: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1
Release date: 2019-09-04
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z30620520 (PDB entry 5QIC)
Macromolecule: Hydroxyacid oxidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.3.15
Sequence length: 369 residues
Sequence: SMLPRLICINDYEQHAKSVLPKSIYDYYRSGANDEETLADNIAAFSRWKLYPRMLRNVAETDLSTSVLGQRVSMPICVGATAMQRMAHVDGELATVRACQSLGTGMMLSSWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQAEKMGYKAIFVTVDTPYLGNRLDDVRNRFKLPPQLRMKNFETSTLSFSPEENFGDDSGLAAYVAKAIDPSISWEDIKWLRRLTSLPIVAKGILRGDDAREAVKHGLNGILVSNHGARQLDGVPATIDVLPEIVEAVEGKVEVFLDGGVRKGTDVLKALALGAKAVFVGRPIVWGLAFQGEKGVQDVLEILKEEFRLAMALSGCQNVKVIDKTLVRKNPLAVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.1887
R free: 0.2061
Average B factor: 17.209
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.75
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Matthews coefficient: 2.36
Solvent content (%): 47.85
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2018-07-18
Bruton's tyrosine kinase in complex with covalent inhibitor compound 10 (PDB entry 8TU3)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLGSKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2276
R free: 0.2767
Average B factor: 27.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: bis-tris pH 6.5, ammonium tartrate, PEG 3350
Matthews coefficient: 2.15
Solvent content (%): 42.69
Ligand: 1-[(4R)-4-{[(6P,8S)-6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrazin-4-yl]oxy}azepan-1-yl]propan-1-one (UEO)
Ligand formula: C19 H24 N6 O2
Ligand molecular weight: 368.433
Ligand SMILES: CCC(=O)N1CCCC(CC1)Oc2c3ccnn3cc(n2)c4cnn(c4)C
Ligand InChI: InChI=1S/C19H24N6O2/c1-3-18(26)24-9-4-5-15(7-10-24)27-19-17-6-8-20-25(17)13-16(22-19)14-11-21-23(2)12-14/h6,8,11-13,15H,3-5,7,9-10H2,1-2H3/t15-/m1/s1
Release date: 2024-06-26
Crystal structure of MYST acetyltransferase domain in complex with inhibitor 60 (PDB entry 6PD9)
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): 2.8
R work: 0.2123
R free: 0.2674
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: 2.54
Solvent content (%): 51.52
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: 2020-04-01
Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ATR kinase inhibitor AZD6738 (PDB entry 7JSP)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 137 residues
Sequence: SMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1733
R free: 0.2049
Average B factor: 37.9774
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.01 M Co(II) chloride, 0.1 M Sodium acetate trihydrate (pH 4.6), 1 M 1,6-Hexanediol
Matthews coefficient: 2.49
Solvent content (%): 50.57
Ligand: 4-(4-{1-[(R)-amino(hydroxy)methyl-lambda~4~-sulfanyl]cyclopropyl}-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine (VJM)
Ligand formula: C20 H26 N6 O2 S
Ligand molecular weight: 414.524
Ligand SMILES: CC1COCCN1c2cc(nc(n2)c3ccnc4c3cc[nH]4)C5(CC5)S(C)(N)O
Ligand InChI: InChI=1S/C20H26N6O2S/c1-13-12-28-10-9-26(13)17-11-16(20(5-6-20)29(2,21)27)24-19(25-17)15-4-8-23-18-14(15)3-7-22-18/h3-4,7-8,11,13,27H,5-6,9-10,12,21H2,1-2H3,(H,22,23)/t13-/m1/s1
Release date: 2021-08-25
Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+ (PDB entry 5UM9)
Macromolecule: Flap endonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 341 residues
Sequence: GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFNGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.805
R work: 0.2078
R free: 0.2659
Average B factor: 122.3541
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 6% MPEG 2K, 10% KCl, 50 mM HEPES pH 7.5, 2.5% Ethylene glycol, 1.06 mM SmSO4
Matthews coefficient: 3.23
Solvent content (%): 61.95
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2017-06-28
Crystal Structure of a human Calcineurin A - Calcineurin B fusion bound to FKBP12 and FK-520 (PDB entry 7U0T)
Macromolecule: Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform,Calcineurin subunit B type 1 fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 244 residues
Sequence: MSGSHHHHHHHHGGENLYFQGSSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICGGGSSGGSTSGGSSGGGGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLDIHKKMVVDV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2111
R free: 0.2604
Average B factor: 50.5788
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 287
Crystal growth procedure: Microlytics MCSG-1 C5: 0.2M Magnesium Acetate, 20% PEG 3,350, HosaA.18272.a.TM11.PD38439 at 20mg/ml + FK-520 (Purified from SEC): cryo: 20% ethylene glycol: tray 318701c5, puck oxo8-2
Matthews coefficient: 2.42
Solvent content (%): 49.27
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: 2022-08-03
HRV14 3C in complex with single chain antibody YDF (PDB entry 6KYZ)
Macromolecule: Genome polyprotein
Type: Protein, polypeptide(L)
Source organism: rhinovirus B14
EC number: 3.4.22.29
Sequence length: 184 residues
Sequence: GSGPNTEFALSLLRKNIMTITTSKGEFTGLGIHDRVCVIPTHAQPGDDVLVNGQKIRVKDKYKLVDPENINLELTVLTLDRNEKFRDIRGFISEDLEGVDATLVVHSNNFTNTILEVGPVTMAGLINLSSTPTNRMIRYDYATKTGQCGGVLCATGKIFGIHVGGNGRQGFSAQLKKQYFVEKQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.845
R work: 0.1745
R free: 0.2081
Average B factor: 23.4076
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M citrate
40% PEG600
Matthews coefficient: 2.59
Solvent content (%): 52.53
Release date: 2020-05-27
Crystal structure of human carbonic anhydrase I in complex with the 1-(2-hydroxy-5-sulfamoylphenyl)-3-[(4-methylphenyl)methyl]urea inhibitor (PDB entry 6F3B)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.20867
R free: 0.24579
Average B factor: 24.911
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 296
Crystal growth procedure: 28% PEG4000, 0.2 M Sodium acetate, Tris 100 mM
Matthews coefficient: 2.32
Solvent content (%): 47.03
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: 2018-10-10
Notum complex with ARUK3003778 (PDB entry 7B50)
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): 1.33
R work: 0.2008
R free: 0.2051
Average B factor: 24.1392
Crystallization method: EVAPORATION
Crystallization pH: 4.2
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate
Matthews coefficient: 1.93
Solvent content (%): 36.37
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: 2022-01-12
Ube2G1 in complex with ubiquitin variant Ubv.G1.1 (PDB entry 6D68)
Macromolecule: Ubiquitin-conjugating enzyme E2 G1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 171 residues
Sequence: SMTELQSALLLRRQLAELNKNPVEGFSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLTFPKDYPLRPPKMKFITEIWHPNVDKNGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISMLADPNGDSPANVDAAKEWREDRNGEFKRKVARCVRKSQETAFE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.2126
R free: 0.2536
Average B factor: 67.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG1500, Succinic acid, Sodium phosphate monobasic monohydrate, Glycine
Matthews coefficient: 2.65
Solvent content (%): 53.52
Release date: 2019-07-17
Crystal structure of the Dbl-homology domain of Bcr-Abl in complex with monobody Mb(Bcr-DH_4). (PDB entry 5N7E)
Macromolecule: Mb(Bcr-DH_4)
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 95 residues
Sequence: SVSSVPTKLEVVAATPTSLLISWDAPAVTVDLYVITYGETGGNSPVQEFEVPGSKSTATISGLKPGVDYTITVYAGSYAYEYYWGPSPISINYRT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.647
R work: 0.1833
R free: 0.2194
Average B factor: 36.1086
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.12 M monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M buffer system 2 pH 7.5 (Sodium HEPES; MOPS (acid)); 50% precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Matthews coefficient: 2.83
Solvent content (%): 56.47
Release date: 2017-12-27
c-KIT kinase domain in complex with avapritinib derivative 10 (PDB entry 8PQD)
Macromolecule: Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: GSMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1746
R free: 0.1943
Average B factor: 34.63
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 285.15
Crystal growth procedure: 6 mg/mL, 10% PEG6000, 200 mM LiCl, 100 mM Tris, pH 8.0, cryo-protected with 20% PEG400 in reservoir directly added to crystallization drop
Matthews coefficient: 1.96
Solvent content (%): 37.24
Ligand: ~{N}-[(1~{S})-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-yl]piperazin-1-yl]pyrimidin-5-yl]ethyl]ethanamide (9VV)
Ligand formula: C28 H29 F N10 O
Ligand molecular weight: 540.595
Ligand SMILES: CC(=O)NC(C)(c1ccc(cc1)F)c2cnc(nc2)N3CCN(CC3)c4c5cc(cn5ncn4)c6cnn(c6)C
Ligand InChI: InChI=1S/C28H29FN10O/c1-19(40)35-28(2,22-4-6-24(29)7-5-22)23-14-30-27(31-15-23)38-10-8-37(9-11-38)26-25-12-20(17-39(25)34-18-32-26)21-13-33-36(3)16-21/h4-7,12-18H,8-11H2,1-3H3,(H,35,40)/t28-/m0/s1
Release date: 2023-12-27
Crystal structure of Fkbp12-IF(SlpA), a chimeric protein of human Fkbp12 and the insert in flap domain of Ecoli SlpA (PDB entry 5I7Q)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A,FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 162 residues
Sequence: GVQVETISPGDGRTFPKRGQTAVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGVPSPDLIQYFSRREFMDAGEPEIGAIMLFTAMDGSEMPGVIREINGDSITVDFNHPLAGQTLVFDVELLKLEAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2033
R free: 0.2383
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25 % PEG1500, 10 % isopropanol, 0.1 M CaCl2, 0.1 M Mes pH 6.5
Matthews coefficient: 2.25
Solvent content (%): 45.29
Release date: 2017-03-08
PP1 Y134K (PDB entry 6OBS)
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: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIKGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.803
R work: 0.2042
R free: 0.2461
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 289
Crystal growth procedure: 20% PEG6000, 1 M lithium chloride, 0.1 M MES, pH 6.0
Matthews coefficient: 2.41
Solvent content (%): 48.94
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: 2019-09-18
ATAD2 in complex with PepLite-Ile (PDB entry 7R05)
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): 1.53
R work: 0.1907
R free: 0.2156
Average B factor: 35.161
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
Complex of ERK2 with 5,7-dihydroxychromone (PDB entry 5WP1)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 357 residues
Sequence: AAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1413
R free: 0.1796
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 290
Crystal growth procedure: 1.1-1.3 M ammonium sulfate, 2% PEG500 MME, 0.1 M HEPES/NaOH, crystals soaked in precipitant solution containing 1.5 mM DHC in 2.5% DMSO for one week
Matthews coefficient: 2.31
Solvent content (%): 46.75
Ligand: 5,7-dihydroxy-4H-1-benzopyran-4-one (B7S)
Ligand formula: C9 H6 O4
Ligand molecular weight: 178.142
Ligand SMILES: c1c(cc2c(c1O)C(=O)C=CO2)O
Ligand InChI: InChI=1S/C9H6O4/c10-5-3-7(12)9-6(11)1-2-13-8(9)4-5/h1-4,10,12H
Release date: 2018-08-08