satarupa22/MacromolecularLigandDB huggingface dataset:
Histone deacetylases complex with peptide macrocycles (PDB entry 6WI3)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 385 residues
Sequence: AAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1966
R free: 0.254
Average B factor: 45.43
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 40% (v/v) PEG600 and 100mM CHES pH 9.5
Matthews coefficient: 2.37
Solvent content (%): 48.01
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: 2021-04-21
Crystal Structure of CK2alpha (PDB entry 5CU6)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.1866
R free: 0.209
Average B factor: 24.44
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.02
Solvent content (%): 39.23
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: 2016-07-27
Structure of USP12-UB-PRG/UAF1 (PDB entry 5L8W)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 376 residues
Sequence: HHHHHHMEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEFYGLTSDISKNSESGYILFYQSRD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.20835
R free: 0.25909
Average B factor: 72.405
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 3.2% PEG4000, 0.1mM MMT pH6.5, 0.1 mM TCEP.

Cryo- 30% Glycerol
Matthews coefficient: 3.08
Solvent content (%): 60.11
Ligand: prop-2-en-1-amine (AYE)
Ligand formula: C3 H7 N
Ligand molecular weight: 57.094
Ligand SMILES: C=CCN
Ligand InChI: InChI=1S/C3H7N/c1-2-3-4/h2H,1,3-4H2
Release date: 2016-09-28
Human Aprataxin (Aptx) V263G bound to RNA-DNA, AMP and Zn product complex (PDB entry 6CVT)
Macromolecule: Aprataxin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.11.7
Sequence length: 182 residues
Sequence: GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHGISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHWTQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.941
R work: 0.2462
R free: 0.2892
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, 20% w/v polyethylene glycol 3350
Matthews coefficient: 2.63
Solvent content (%): 53.16
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2018-07-04
WWE domain of human HUWE1 (PDB entry 6MIW)
Macromolecule: E3 ubiquitin-protein ligase HUWE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 91 residues
Sequence: GQSNSNNWRWFDDRSGRWCSYSASNNSTIDSAWKSGETSVRFTAGRRRYTVQFTTMVQVNEETGNRRPVMLTLLRVPRLNKNSKNSNGQEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1798
R free: 0.2118
Average B factor: 28.326
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: Molecular Dimensions Morpheus HT condition D3
Matthews coefficient: 2.64
Solvent content (%): 53.48
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2018-10-17
Human Aldose Reductase complexed with a ligand with an IDD structure at 1.20 A (1) (PDB entry 4RPQ)
Macromolecule: Aldose reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.21
Sequence length: 315 residues
Sequence: ASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1421
R free: 0.1645
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+=0.66 g/L and Human Aldose Reductase= 15 mg/ml. Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) PEG6000 saturated with the inhibitor., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.18
Solvent content (%): 43.59
Ligand: ({3-[(3-nitrobenzyl)carbamoyl]biphenyl-4-yl}oxy)acetic acid (3UH)
Ligand formula: C22 H18 N2 O6
Ligand molecular weight: 406.388
Ligand SMILES: c1ccc(cc1)c2ccc(c(c2)C(=O)NCc3cccc(c3)[N+](=O)[O-])OCC(=O)O
Ligand InChI: InChI=1S/C22H18N2O6/c25-21(26)14-30-20-10-9-17(16-6-2-1-3-7-16)12-19(20)22(27)23-13-15-5-4-8-18(11-15)24(28)29/h1-12H,13-14H2,(H,23,27)(H,25,26)
Release date: 2015-11-18
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434899 (PDB entry 5RWB)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1794
R free: 0.2068
Average B factor: 19.379
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.09
Solvent content (%): 41.17
Ligand: 1-[(thiophen-3-yl)methyl]piperidin-4-ol (T0Y)
Ligand formula: C10 H15 N O S
Ligand molecular weight: 197.297
Ligand SMILES: c1cscc1CN2CCC(CC2)O
Ligand InChI: InChI=1S/C10H15NOS/c12-10-1-4-11(5-2-10)7-9-3-6-13-8-9/h3,6,8,10,12H,1-2,4-5,7H2
Release date: 2020-11-11
Crystal structure of phosphatidyl inositol 4-kinase II alpha in the apo state (PDB entry 5EUT)
Macromolecule: Phosphatidylinositol 4-kinase type 2-alpha,Endolysin,Phosphatidylinositol 4-kinase type 2-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.67
Sequence length: 556 residues
Sequence: GAMGTVAAQAQALAAQAAAAAHAAQAHRERNEFPEDPEFEAVVRQAELAIERCIFPERIYQGSSGSYFVKDPQGRIIAVFKPKNEEPYGHLNPKWTKWLQKGTGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLGRDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEKVPKVGQRFNRIGLPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLLQFERLVVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWRAYPFYWAWLPQAKVPFSQEIKDLILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQILNLTQALKDNKSPLHLVQMPPVIVETARSHQRSSSESYTQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.802
R work: 0.2464
R free: 0.2889
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 M bicine/Trizma base pH 8.5
Matthews coefficient: 2.51
Solvent content (%): 50.97
Release date: 2015-12-23
HLA-E*01:03 in complex with Mtb14 (PDB entry 7P49)
Macromolecule: HLA class I histocompatibility antigen, alpha chain E
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 276 residues
Sequence: GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2373
R free: 0.2791
Average B factor: 42.02
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3 M AS, 0.1 M MES pH 6
Matthews coefficient: 2.22
Solvent content (%): 44.7
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: 2022-06-22
Crystal Structure of human cyclic GMP-AMP synthase (PDB entry 7FU5)
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): 2.18
R work: 0.2206
R free: 0.2784
Average B factor: 51.2282
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: 2.48
Solvent content (%): 50.31
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
Crystal structure of human Fibrillarin in ligand-free state (PDB entry 7SE6)
Macromolecule: rRNA 2'-O-methyltransferase fibrillarin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 242 residues
Sequence: SNAGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKVKN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.2263
R free: 0.2595
Average B factor: 50.34
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.75-3.3 M Sodium Formate
Matthews coefficient: 2.98
Solvent content (%): 58.71
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2022-02-09
Crystal structure of FGFR1 kinase domain in complex with 7n (PDB entry 4ZSA)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 308 residues
Sequence: AGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2036
R free: 0.2541
Average B factor: 42.8897
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Bis-Tris pH 6.5, 0.3M (NH4)2SO4, 15-20% PEG10000, 5% EG
Matthews coefficient: 2.67
Solvent content (%): 54.01
Ligand: 4-(4-ethylpiperazin-1-yl)-N-[6-(3-methoxyphenyl)-2H-indazol-3-yl]benzamide (4UT)
Ligand formula: C27 H29 N5 O2
Ligand molecular weight: 455.551
Ligand SMILES: CCN1CCN(CC1)c2ccc(cc2)C(=O)Nc3c4ccc(cc4n[nH]3)c5cccc(c5)OC
Ligand InChI: InChI=1S/C27H29N5O2/c1-3-31-13-15-32(16-14-31)22-10-7-19(8-11-22)27(33)28-26-24-12-9-21(18-25(24)29-30-26)20-5-4-6-23(17-20)34-2/h4-12,17-18H,3,13-16H2,1-2H3,(H2,28,29,30,33)
Release date: 2015-06-17
CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-37 A.K.A 7-(1-phenyl-3-(((1S,3S)-3-phenyl-2,3-dihydro-1H-inden-1-yl)amino)propyl)-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine (PDB entry 6WY5)
Macromolecule: Myeloperoxidase light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.2.2
Sequence length: 105 residues
Sequence: CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.898
R work: 0.2222
R free: 0.245
Average B factor: 97.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen
Matthews coefficient: 2.68
Solvent content (%): 54.15
Ligand: HEME C (HEC)
Ligand formula: C34 H34 Fe N4 O4
Ligand molecular weight: 618.503
Ligand SMILES: CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
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,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
Release date: 2020-10-14
Human DNA polymerase eta R61A-DNA ternary complex: reaction with 1 mM Mg2+ for 40s (PDB entry 5KFT)
Macromolecule: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 12 residues
Sequence: CATTATGACGCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.182
R free: 0.211
Average B factor: 23.8
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.1
Solvent content (%): 41.35
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: 2016-06-22
LTA4 hydrolase (E297Q) mutant in complex with Pro-Gly-Pro peptide (PDB entry 6ENB)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 611 residues
Sequence: GPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHQISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1554
R free: 0.1861
Average B factor: 27.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 8000, 0.1 IMIDAZOLE PH 6.8, 0.1 M SODIUM ACETATE, 0.005 M YBCL3
Matthews coefficient: 2.41
Solvent content (%): 49.06
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2017-12-13
Discovery of the first orally bioavailable ADAMTS7 inhibitor BAY-9835 (PDB entry 8RIJ)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 158 residues
Sequence: GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.17279
R free: 0.21904
Average B factor: 30.522
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: not known
Matthews coefficient: 2.37
Solvent content (%): 48.1
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
The crystal structure of MLL2 in complex with ASH2L and RBBP5 (PDB entry 7BRE)
Macromolecule: Set1/Ash2 histone methyltransferase complex subunit ASH2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 184 residues
Sequence: SRVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTISGRGSSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.803
R work: 0.2185
R free: 0.2646
Average B factor: 52.2977
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Matthews coefficient: 2.32
Solvent content (%): 46.92
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: 2020-07-22
Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol (PDB entry 6FUI)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 232 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.13232
R free: 0.1978
Average B factor: 18.542
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22-25% PEG3350, 100 mM HEPES pH 7.5
Matthews coefficient: 2.12
Solvent content (%): 41.95
Ligand: (1~{R},2~{S})-2-[[4-[[3-(aminomethyl)phenyl]amino]quinazolin-2-yl]amino]cyclohexane-1-carboxylic acid (E7W)
Ligand formula: C22 H25 N5 O2
Ligand molecular weight: 391.466
Ligand SMILES: c1ccc2c(c1)c(nc(n2)NC3CCCCC3C(=O)O)Nc4cccc(c4)CN
Ligand InChI: InChI=1S/C22H25N5O2/c23-13-14-6-5-7-15(12-14)24-20-16-8-1-3-10-18(16)25-22(27-20)26-19-11-4-2-9-17(19)21(28)29/h1,3,5-8,10,12,17,19H,2,4,9,11,13,23H2,(H,28,29)(H2,24,25,26,27)/t17-,19+/m1/s1
Release date: 2018-06-06
Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 0.12 mM Mn2+ for 600s (PDB entry 7U7Z)
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): 1.67
R work: 0.1863
R free: 0.219
Average B factor: 33.3811
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.2
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2022-05-04