satarupa22/MacromolecularLigandDB huggingface dataset:
CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) in complex with ferrous heme and tryptophan (PDB entry 6E46)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 405 residues
Sequence: MGSSHHHHHHSSGSAAYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSAALELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.2075
R free: 0.2474
Average B factor: 44.6973
Crystallization method: EVAPORATION
Crystallization pH: 6.2
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350
Matthews coefficient: 2.48
Solvent content (%): 50.46
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: 2018-11-14
DNA Polymerase Mu Product Complex, 10 mM Mg2+ (60 min) (PDB entry 5TYE)
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): 2.047
R work: 0.1858
R free: 0.2282
Average B factor: 27.3899
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: 2.68
Solvent content (%): 54.02
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-08-30
Crystal structure of human carbonic anhydraseisozyme II with 3-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide (PDB entry 5DRS)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.144
R free: 0.173
Average B factor: 17.214
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 1.99
Solvent content (%): 37.7
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: 2016-09-28
Carbonic Anhydrase IX Mimic Complexed with N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)propionamide (PDB entry 7JO0)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.607
R work: 0.154
R free: 0.183
Average B factor: 17.8422
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris
Matthews coefficient: 2.05
Solvent content (%): 39.93
Ligand: N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)propanamide (VFG)
Ligand formula: C5 H8 N4 O3 S2
Ligand molecular weight: 236.272
Ligand SMILES: CCC(=O)Nc1nnc(s1)S(=O)(=O)N
Ligand InChI: InChI=1S/C5H8N4O3S2/c1-2-3(10)7-4-8-9-5(13-4)14(6,11)12/h2H2,1H3,(H2,6,11,12)(H,7,8,10)
Release date: 2020-11-04
Crystal structure of the MLL3-Ash2L-RbBP5 complex (PDB entry 5F6K)
Macromolecule: Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 184 residues
Sequence: SRVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTISGRGSSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMG
Oligomeric state: Hetero 7-mer
Stoichiometry: A2, B2, C2, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.411
R work: 0.1804
R free: 0.2284
Average B factor: 46.5872
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Matthews coefficient: 2.47
Solvent content (%): 50.16
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: 2016-02-24
Crystal structure of DUSP22 mutant_N128D (PDB entry 6LOT)
Macromolecule: Dual specificity protein phosphatase 22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 157 residues
Sequence: GPMGNGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSARPMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPDVGFQRQLQEFEKHEVHQYRQWLKEEYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1919
R free: 0.2192
Average B factor: 25.5385
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M PIPES, 30% PEG 3,350, 0.2 M Li2SO4
Matthews coefficient: 2.64
Solvent content (%): 53.39
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: 2020-10-28
Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an Orally Active Renin Inhibitor (PDB entry 5TMK)
Macromolecule: Renin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.15
Sequence length: 337 residues
Sequence: GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1978
R free: 0.2356
Average B factor: 74.423
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.9
Crystallization temperature (K): 293
Crystal growth procedure: 23% PEG600, 0.06M citrate, 0.04M citric acid
Matthews coefficient: 3.08
Solvent content (%): 60.02
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: 2017-10-18
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3-pyridin-3-ylaniline (N05798a) (ligand modelled based on PANDDA event map) (PDB entry 5FYY)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGAKDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.1867
R free: 0.2216
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.11
Solvent content (%): 41.61
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: 2016-03-23
Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a T (PDB entry 8VFE)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1999
R free: 0.2349
Average B factor: 32.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
Matthews coefficient: 2.4
Solvent content (%): 48.7
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2024-05-08
Crystal structure of the human 8-oxoguanine glycosylase (OGG1) processed with the CrystalDirect automated mounting and cryo-cooling technology (PDB entry 5AN4)
Macromolecule: N-GLYCOSYLASE/DNA LYASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.23
Sequence length: 312 residues
Sequence: GHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.18362
R free: 0.21427
Average B factor: 18.633
Crystal growth procedure: 0.1 M SODIUM CITRATE, PH=5.5, 0.2 M AMMONIUM SULFATE, 24 % PEG 3350
Matthews coefficient: 2.19
Solvent content (%): 43.8
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: 2016-04-13
Crystal structure of human phosphodiesterase 2A with N-(1-adamantyl)-1-(2-chloro-5-isobutoxy-phenyl)-4-methyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (PDB entry 6C7G)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 342 residues
Sequence: SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1973
R free: 0.2335
Average B factor: 23.7675
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 17-19% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris, pH 8.4
Matthews coefficient: 2.26
Solvent content (%): 45.46
Ligand: 1-[2-chloro-5-(2-methylpropoxy)phenyl]-4-methyl-N-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl][1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (EOY)
Ligand formula: C31 H34 Cl N5 O2
Ligand molecular weight: 544.087
Ligand SMILES: Cc1c2nnc(n2c3cc(ccc3n1)C(=O)NC45CC6CC(C4)CC(C6)C5)c7cc(ccc7Cl)OCC(C)C
Ligand InChI: InChI=1S/C31H34ClN5O2/c1-17(2)16-39-23-5-6-25(32)24(12-23)29-36-35-28-18(3)33-26-7-4-22(11-27(26)37(28)29)30(38)34-31-13-19-8-20(14-31)10-21(9-19)15-31/h4-7,11-12,17,19-21H,8-10,13-16H2,1-3H3,(H,34,38)/t19-,20+,21-,31-
Release date: 2018-08-15
Human cyclic GMP-AMP synthase (cGAS) in complex with Compound F1 (PDB entry 5VDW)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 363 residues
Sequence: MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.711
R work: 0.2223
R free: 0.2571
Average B factor: 61.5127
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 18-20% PEG 3350, 0.2 M ammonium citrate pH 7
Matthews coefficient: 2.52
Solvent content (%): 51.24
Ligand: [2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-yl]acetic acid (9BY)
Ligand formula: C12 H9 N3 O2 S
Ligand molecular weight: 259.284
Ligand SMILES: c1ccc2c(c1)nc(n2CC(=O)O)c3cscn3
Ligand InChI: InChI=1S/C12H9N3O2S/c16-11(17)5-15-10-4-2-1-3-8(10)14-12(15)9-6-18-7-13-9/h1-4,6-7H,5H2,(H,16,17)
Release date: 2017-09-27
Crystal structure of KLK6 in complex with compound 17a (PDB entry 7QFV)
Macromolecule: Kallikrein-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 223 residues
Sequence: LVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVFLGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSELIQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHAYPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGNIPCGSKEKPGVYTNVCRYTNWIQKTIQAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1761
R free: 0.2112
Average B factor: 22.8981
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.20 M trimethylamine N-oxide, 0.1 M Tris-HCl pH8.5, 20% PEG MME 2000
Matthews coefficient: 1.92
Solvent content (%): 36.02
Release date: 2022-10-26
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[2-[3-[[(5-bromo-2-hydroxybenzoyl)amino]methyl]anilino]-1,3-thiazol-4-yl]acetic acid (PDB entry 7FTZ)
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): 2.5
R work: 0.223
R free: 0.272
Average B factor: 71.84
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: 2.52
Solvent content (%): 51.27
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2024-02-21
Structure of RNF125 in complex with UbcH5b (PDB entry 8GBQ)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 152 residues
Sequence: GPLGSMALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1839
R free: 0.201
Average B factor: 45.1628
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M CHES 9.5
20% PEG 8000
Matthews coefficient: 2.62
Solvent content (%): 53.08
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: 2023-07-19
Human renin in complex with compound3 (PDB entry 7XGP)
Macromolecule: Renin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.15
Sequence length: 340 residues
Sequence: LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1983
R free: 0.2542
Average B factor: 69.423
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Na citrate pH4.2, 30% PEG3350, 0.6M NaCl
Matthews coefficient: 3.14
Solvent content (%): 60.77
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: 2022-09-07
Crystal Structure of human phosphodiesterase 10 in complex with N-[(5,8-dimethyl-[1,2,4]triazolo[1,5-a]pyrazin-2-yl)methyl]-N,2-dimethyl-5-phenyl-1,2,4-triazol-3-amine (PDB entry 5SHR)
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): 1.98
R work: 0.182
R free: 0.2301
Average B factor: 38.36
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: 2.62
Solvent content (%): 52.97
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: 2022-10-19
Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man long peptide) (PDB entry 7E9K)
Macromolecule: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.4.1.312
Sequence length: 539 residues
Sequence: GAPPAPALRIDYPKALQILTEGGTHMVCTGRTHTDRLCRFKWLCYSSEAEEFIFFHGNASVMLPSLGSRRFQPALLDLSTVEDHNTQYFNFVELPAAALRFMPKPVFVPDVALIANRFNPDNLMHVFHDDLLPLFYTLRQFPGLAREARLFFMEGWGEGAHFDLYKLLSPKQPLLRAQLKALGRLLCFSHAFVGLSKVTTWYQYGFVQPQGPKANILVSGNEIRQFAHFLMEKLNVSQAGGPLGEEYILVFSRTQNRLILNEAELLLALAQEFQMKTVTVSLEDHAFADVVRLVSNASMLVSMHGAQLVTALFLPRGAAVVELFPYAVNPDHYTPYKTLATLPGMDLQYIAWQNTMPENTVTHPERPWDQGGIAHLDRAEQARILQSREVPRHLCCRNPEWLFRIYQDTKVDIPSLIQTIRRVVKGHPGPRKQKWTVSLYPGKVREARCQASVQGASEARLSVSWQIPWNLKYLKVREVKYEVWLQEQGENTYVPYMLALQNHTFTENIKPFTTYLVWIRCIFNKTLLGPFADVLVCST
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2022
R free: 0.2407
Average B factor: 40.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris-HCl (pH 8.0 or 8.5), 12-16% PEG 8000, 1% tacsimate (pH 7.0)
Matthews coefficient: 2.66
Solvent content (%): 53.77
Ligand: alpha-D-mannopyranose (MAN)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1
Release date: 2021-05-05
Human carbonic anhydrase II with bound IrCp* complex (cofactor 10) to generate an artificial transfer hydrogenase (ATHase) (PDB entry 6QFX)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MAHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.32
R work: 0.1722
R free: 0.1974
Average B factor: 22.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.9
Crystallization temperature (K): 293
Crystal growth procedure: 2.6 M ammonium sulfate, 50 mM Tris-H2SO4
Matthews coefficient: 2.15
Solvent content (%): 42.69
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: 2019-04-17