satarupa22/MacromolecularLigandDB huggingface dataset:
Structure the proprotein convertase furin in complex with meta-guanidinomethyl-Phac-RVR-Amba at 2.0 Angstrom resolution. (PDB entry 5JXH)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1566
R free: 0.1853
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: crystallization solution: 100 mM MES, 200 mM K/NaH2PO4, pH 5.5-6.0, 3-4 M NaCl, 3% DMSO; reservoir solution: 3-4 M NaCl
Matthews coefficient: 3.67
Solvent content (%): 66.49
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: 2016-10-05
Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group (PDB entry 7OWD)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase CYLD
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 86 residues
Sequence: SHGLEVGSLAEVKENPPFYGVIRWIGQPPGLNEVLAGLELEDECAGCTDGTFRGTRYFTCALKKALFVKLKSCRPDSRFASLQPVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.2136
R free: 0.245
Average B factor: 52.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 291
Crystal growth procedure: 40 (v/v) PEG 300, 100 mM phosphate/citrate pH 4.2
Matthews coefficient: 2.02
Solvent content (%): 39
Release date: 2021-10-20
DCN1 bound to 8 (PDB entry 6XOM)
Macromolecule: Lysozyme, DCN1-like protein 1 chimera
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 386 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNAMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWAEAAVNLAKSRWYNQTPNRTKRVITTFATGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.195
R free: 0.243
Average B factor: 31.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 28 - 33% PEG 3350, 200 mM ammonium formate
Matthews coefficient: 2.07
Solvent content (%): 40.63
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2021-06-02
Crystal structure of ethyl-paraoxon inhibited recombinant human bile salt activated lipase (aged form) (PDB entry 6H19)
Macromolecule: Bile salt-activated lipase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.13
Sequence length: 547 residues
Sequence: HHHHHHHHENLYFQSKLGAVYTEGGFVEGVNKKLGLLGDSVDIFKGIPFAAPTKALENPQPHPGWQGTLKAKNFKKRCLQATITQDSTYGDEDCLYLNIWVPQGRKQVSRDLPVMIWIYGGAFLMGSGHGANFLNNYLYDGEEIATRGNVIVVTFNYRVGPLGFLSTGDANLPGNYGLRDQHMAIAWVKRNIAAFGGDPDNITLFGESAGGASVSLQTLSPYNKGLIRRAISQSGVALSPWVIQKNPLFWAKKVAEKVGCPVGDAARMAQCLKVTDPRALTLAYKVPLAGLEYPMLHYVGFVPVIDGDFIPDDPINLYANAADIDYIAGTNNMDGHIFASIDMPAINKGNKKVTEEDFYKLVSEFTITKGLRGAKTTFDVYTESWAQDPSQENKKKTVVDFETDVLFLVPTEIALAQHRANAKSAKTYAYLFSHPSRMPVYPKWVGADHADDIQYVFGKPFATPTGYRPQDRTVSKAMIAYWTNFAKTGDPNMGDSAVPTHWEPYTTENSGYLEITKKMGSSSMKRSLRTNFLRYWTLTYLALPTVT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.193
R free: 0.2296
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 8000, cacodylate, zinc acetate
Matthews coefficient: 2.48
Solvent content (%): 50.46
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-03-27
Crystal Structure of human phosphodiesterase 10 in complex with ethyl 1-[3-[3-(4-ethoxycarbonyl-5-methyl-imidazol-1-yl)phenoxy]phenyl]-5-methyl-imidazole-4-carboxylate (PDB entry 5SKS)
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): 2.31
R work: 0.1548
R free: 0.214
Average B factor: 39.278
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: 2.61
Solvent content (%): 52.94
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: 2022-10-12
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-617 (PDB entry 7AAG)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1667
R free: 0.1967
Average B factor: 30.396
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene glycol, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.63
Solvent content (%): 53.25
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: 2021-10-06
Development of a novel class of potent and selective FIXa inhibitors (PDB entry 4ZAE)
Macromolecule: Coagulation factor IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.22
Sequence length: 235 residues
Sequence: VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGASALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1477
R free: 0.1741
Average B factor: 32.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 295
Crystal growth procedure: 50 mM CHES, pH 9.0, 1.3 M tri-sodium citrate and 3 mM compound (cross seeded with crystals grown from 50 mM Tris, pH 7.2, 1.45 M ammonium sulfate, 2.0 M sodium chloride and 3 mM compound)
Matthews coefficient: 2.82
Solvent content (%): 56.33
Ligand: 2,6-dichloro-N-[(2R)-2-(5,6-dimethyl-1H-benzimidazol-2-yl)-2-phenylethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide (4M1)
Ligand formula: C26 H22 Cl2 N6 O
Ligand molecular weight: 505.398
Ligand SMILES: Cc1cc2c(cc1C)nc([nH]2)C(CNC(=O)c3c(cc(cc3Cl)n4cnnc4)Cl)c5ccccc5
Ligand InChI: InChI=1S/C26H22Cl2N6O/c1-15-8-22-23(9-16(15)2)33-25(32-22)19(17-6-4-3-5-7-17)12-29-26(35)24-20(27)10-18(11-21(24)28)34-13-30-31-14-34/h3-11,13-14,19H,12H2,1-2H3,(H,29,35)(H,32,33)/t19-/m0/s1
Release date: 2015-06-03
Crystal structure of KDM4D with tetrazole compound 4 (PDB entry 6ETT)
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): 1.257
R work: 0.1229
R free: 0.1455
Average B factor: 19.0742
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350
Matthews coefficient: 2.53
Solvent content (%): 51.39
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: 2019-02-20
human POGLUT1 in complex with EGF(+) and UDP (PDB entry 5L0T)
Macromolecule: Protein O-glucosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1
Sequence length: 357 residues
Sequence: GSKWKVFIDQINRSLENYEPCSSQNCSCYHGVIEEDLTPFRGGISRKMMAEVVRRKLGTHYQITKNRLYRENDCMFPSRCSGVEHFILEVIGRLPDMEMVINVRDYPQVPKWMEPAIPVFSFSKTSEYHDIMYPAWTFWEGGPAVWPIYPTGLGRWDLFREDLVRSAAQWPWKKKNSTAYFRGSRTSPERDPLILLSRKNPKLVDAEYTKNQAWKSMKDTLGKPAAKDVHLVDHCKYKYLFNFRGVAASFRFKHLFLCGSLVFHVGDEWLEFFYPQLKPWVHYIPVKTDLSNVQELLQFVKANDDVAQEIAERGSQFIRNHLQMDDITCYWENLLSEYSKFLSYNVTRRKGYDQIIP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1561
R free: 0.1734
Average B factor: 30.8524
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG5000 MME, 50 mM MES pH 6.5, 10mM CaCl2, 250mM NaCl, 5% glycerol
Matthews coefficient: 2.42
Solvent content (%): 49.16
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: 2017-08-09
Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 120 s (PDB entry 5VS4)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACAGGCGCATCAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1988
R free: 0.2569
Average B factor: 26.703
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.78
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: 2017-07-19
Crystal structure of human dihydroorotate dehydrogenase at 1.7 A resolution (PDB entry 5K9D)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 368 residues
Sequence: SMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1363
R free: 0.1601
Average B factor: 19.4203
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.8
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M sodium acetate trihydrate pH 4.8
1.8 M ammonium sulfate
30% (v/v) glycerol
Matthews coefficient: 3.46
Solvent content (%): 64.5
Ligand: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL (FNR)
Ligand formula: C17 H23 N4 O9 P
Ligand molecular weight: 458.36
Ligand SMILES: Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H23N4O9P/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/h3-4,11-12,14,18,22-24H,5-6H2,1-2H3,(H2,27,28,29)(H2,19,20,25,26)/t11-,12+,14-/m0/s1
Release date: 2016-10-12
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-587-558 (PDB entry 5QQJ)
Macromolecule: Ras-related C3 botulinum toxin substrate 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 178 residues
Sequence: SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2118
R free: 0.2687
Average B factor: 37.634
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M bis-tris pH 5.5 24% PEG 3350
Matthews coefficient: 2.35
Solvent content (%): 47.72
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-12-18
Post-catalytic complex of human Polymerase Mu (W434A) mutant with incoming dTTP (PDB entry 5VZF)
Macromolecule: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 9 residues
Sequence: CGGCATACG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1694
R free: 0.1952
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 90mM HEPES pH 7.5, 18% PEG4K
Matthews coefficient: 2.85
Solvent content (%): 56.8
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2017-07-05
Carbonic Anhydrase IX-mimic in complex with aryloxy-2-hydroxypropylammine sulfonamide (PDB entry 5WLT)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1452
R free: 0.1758
Average B factor: 18.2664
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M Sodium Citrate
50mM Tris-HCl
Matthews coefficient: 2.16
Solvent content (%): 42.96
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: 2018-08-01
Crystal structure of chimeric omicron RBD (strain BA.2) complexed with human ACE2 (PDB entry 7UFK)
Macromolecule: Angiotensin-converting enzyme 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.23
Sequence length: 597 residues
Sequence: STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1919
R free: 0.2353
Average B factor: 77.96
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM Tris, pH 8.5, 18-22% PEG6000, 100 mM sodium chloride
Matthews coefficient: 2.86
Solvent content (%): 56.99
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
Human DNA Pol eta S113A with dA-ended primer and dATP: in crystallo reaction for 230 s (PDB entry 7M87)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERAAIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.2005
R free: 0.2276
Average B factor: 24.6272
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG 2000 MME,
100 mM MES
Matthews coefficient: 2.08
Solvent content (%): 40.76
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: 2021-06-02
Crystal structure of Harmonin-homology domain 2 (HHD2) of human RTEL1 (PDB entry 7WU8)
Macromolecule: Regulator of telomere elongation helicase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 96 residues
Sequence: MGSSHHHHHHSGQHAVSAYLADARRALGSAGCSQLLAALTAYKQDDDLDKVLAVLAALTTAKPEDFPLLHRFSMFVRPHHKQRFSQTCTDLTGRPY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.599
R work: 0.1765
R free: 0.2012
Average B factor: 27.133
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 20mM Tris pH7.4, 250mM NaCl, 5% Glycerol
Matthews coefficient: 2.14
Solvent content (%): 42.4
Release date: 2023-08-09
Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) at N-1 of the template base paired with incoming dTTP (PDB entry 7MZ8)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2013
R free: 0.2634
Average B factor: 47.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.38
Solvent content (%): 48.37
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-06-01
Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor (PDB entry 7FD0)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: GASMQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2311
R free: 0.2655
Average B factor: 32.6319
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.25 M ammonium iodide, 0.03 M glycyl-glycyl-glycine and 15-25% PEG3350
Matthews coefficient: 2.15
Solvent content (%): 42.86
Ligand: N-[(3S)-5-methyl-7-[2-(oxan-4-yl)ethynyl]-4-oxidanylidene-2,3-dihydro-1,5-benzoxazepin-3-yl]-5-(phenylmethyl)-4H-1,2,4-triazole-3-carboxamide (3IU)
Ligand formula: C27 H27 N5 O4
Ligand molecular weight: 485.534
Ligand SMILES: CN1c2cc(ccc2OCC(C1=O)NC(=O)c3[nH]c(nn3)Cc4ccccc4)C#CC5CCOCC5
Ligand InChI: InChI=1S/C27H27N5O4/c1-32-22-15-20(8-7-18-11-13-35-14-12-18)9-10-23(22)36-17-21(27(32)34)28-26(33)25-29-24(30-31-25)16-19-5-3-2-4-6-19/h2-6,9-10,15,18,21H,11-14,16-17H2,1H3,(H,28,33)(H,29,30,31)/t21-/m0/s1
Release date: 2022-01-19