satarupa22/MacromolecularLigandDB huggingface dataset:
Human DNA polymerase eta-DNA ternary complex: reaction with 10 mM Mn2+ for 600s (PDB entry 5KFL)
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): 1.65
R work: 0.1715
R free: 0.2083
Average B factor: 30.1366
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.08
Solvent content (%): 41.01
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: 2016-06-22
Factor VIIA in complex with the inhibitor (2R,15R)-2-[(1-aminoisoquinolin-6-yl)amino]-8-fluoro-7-hydroxy-4,15,17-trimethyl-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaene-3,12-dione (PDB entry 5I46)
Macromolecule: Coagulation factor VII (Heavy Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.2171
R free: 0.2386
Average B factor: 36.71
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000
Matthews coefficient: 3.9
Solvent content (%): 68.47
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: 2016-06-22
PDE2 in complex with molecule 5 (PDB entry 6EZF)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 353 residues
Sequence: MHASDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEELEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.15135
R free: 0.19804
Average B factor: 17.619
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.25
Crystallization temperature (K): 298
Crystal growth procedure: 25 % PEG4000
0.10 M Tris 8.25
0.20 M LiSO4
Matthews coefficient: 2.4
Solvent content (%): 48.85
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: 2018-04-04
Kallikrein-related peptidase 8 leupeptin inhibitor complex (PDB entry 5MS4)
Macromolecule: Kallikrein-8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.118
Sequence length: 228 residues
Sequence: VLGGHECQPHSQPWQAALFQGQQLLCGGVLVGGNWVLTAAHCKKPKYTVRLGDHSLQNKDGPEQEIPVVQSIPHPCYNSSDVEDHNHDLMLLQLRDQASLGSKVKPISLADHCTQPGQKCTVSGWGTVTSPRENFPDTLNCAEVKIFPQKKCEDAYPGQITDGMVCAGSSKGADTCQGDSGGPLVCDGALQGITSWGSDPCGRSDKPGVYTNICRYLDWIKKIIGSKG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.212
R free: 0.259
Average B factor: 16.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: 35% (v/v) tert-Butanol, 0.1 M tri-Na citrate/citric acid
Matthews coefficient: 1.98
Solvent content (%): 37.99
Ligand: TERTIARY-BUTYL ALCOHOL (TBU)
Ligand formula: C4 H10 O
Ligand molecular weight: 74.122
Ligand SMILES: CC(C)(C)O
Ligand InChI: InChI=1S/C4H10O/c1-4(2,3)5/h5H,1-3H3
Release date: 2018-01-17
Structure of human TUT7 catalytic module (CM) (PDB entry 5W0B)
Macromolecule: Terminal uridylyltransferase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.52
Sequence length: 389 residues
Sequence: GAGAGSKRIQLEPLPPLTPKFLNILDQVCIQCYKDFSPTIIEDQAREHIRQNLESFIRQDFPGTKLSLFGSSKNGFGFKQSDLAVCMTINGLETAEGLDCVRTIEELARVLRKHSGLRNILPITTAKVPIVKFFHLRSGLEVDISLYNTLALHNTRLLSAYSAIDPRVKYLCYTMKVFTKMCDIGDASRGSLSSYAYTLMVLYFLQQRNPPVIPVLQEIYKGEKKPEIFVDGWNIYFFDQIDELPTYWSECGKNTESVGQLWLGLLRFYTEEFDFKEHVISIRRKSLLTTFKKQWTSKYIVIEDPFDLNHNLGAGLSRKMTNFIMKAFINGRRVFGIPVKGFPKDYPSKMEYFFDPDVLTEGELAPNDRCCRICGKIGHFMKDCPMRRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.614
R work: 0.2305
R free: 0.255
Average B factor: 95.1683
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6
Matthews coefficient: 3.74
Solvent content (%): 67.12
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: 2017-06-28
MAGI-1 complexed with a pRSK1 peptide (PDB entry 5N7F)
Macromolecule: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 427 residues
Sequence: GSMGKPFFTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRGYPLGSSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1862
R free: 0.2401
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 296
Crystal growth procedure: 14% PEG 8000, 200 mM MgCl2, 100 mM TRIS
Matthews coefficient: 2.92
Solvent content (%): 57.93
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: 2017-11-08
Crystal structure of the titin domain Fn3-11 (PDB entry 8OS3)
Macromolecule: Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 107 residues
Sequence: GSSSPPSPPLDLHVTDAGRKHIAIAWKPPEKNGGSPIIGYHVEMCPVGTEKWMRVNSRPIKDLKFKVEEGVVPDKEYVLRVRAVNAIGVSEPSEISENVVAKDPDCK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1657
R free: 0.2082
Average B factor: 26.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30mM HEPES pH 7.5
50mM NaCl
0.5mM DTT
100mM sodium acetate pH 4.5
200mM Lithium sulphate
50% v/v PEG 400
Matthews coefficient: 1.98
Solvent content (%): 37.91
Release date: 2023-08-23
Crystal structure of human WEE1 kinase domain in complex with RAC-IV-101, a MK1775 analogue (PDB entry 5VDA)
Macromolecule: Wee1-like protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: GAGSMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1906
R free: 0.2554
Average B factor: 46.0356
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 291
Crystal growth procedure: 5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-101
Matthews coefficient: 2.19
Solvent content (%): 43.8
Ligand: 1-{6-[(1S)-1-hydroxyethyl]pyridin-2-yl}-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one (98D)
Ligand formula: C26 H30 N8 O2
Ligand molecular weight: 486.569
Ligand SMILES: CC(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O
Ligand InChI: InChI=1S/C26H30N8O2/c1-4-12-33-25(36)21-17-27-26(30-24(21)34(33)23-7-5-6-22(29-23)18(2)35)28-19-8-10-20(11-9-19)32-15-13-31(3)14-16-32/h4-11,17-18,35H,1,12-16H2,2-3H3,(H,27,28,30)/t18-/m0/s1
Release date: 2018-04-04
Crystal structure of MKK7 (MAP2K7) in complex with ASC69 (PDB entry 6YG5)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 307 residues
Sequence: SMKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2307
R free: 0.2815
Average B factor: 77.071
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 277.15
Crystal growth procedure: 16% PEG3350, 0.2 M ammonium acetate, 
0.1 M tris, pH 7.8
Matthews coefficient: 2.46
Solvent content (%): 49.94
Ligand: [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]quinazolin-2-yl}amino)phenyl]acetonitrile (IHH)
Ligand formula: C22 H19 N7
Ligand molecular weight: 381.433
Ligand SMILES: c1ccc2c(c1)c(nc(n2)Nc3ccc(cc3)CC#N)Nc4cc([nH]n4)C5CC5
Ligand InChI: InChI=1S/C22H19N7/c23-12-11-14-5-9-16(10-6-14)24-22-25-18-4-2-1-3-17(18)21(27-22)26-20-13-19(28-29-20)15-7-8-15/h1-6,9-10,13,15H,7-8,11H2,(H3,24,25,26,27,28,29)
Release date: 2020-08-12
Crystal structure of LSD2 in complex with trans-4-Br-PCPA (PDB entry 7XE2)
Macromolecule: Lysine-specific histone demethylase 1B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 793 residues
Sequence: AKKKATETTDEDEDGGSEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.167
R free: 0.194
Average B factor: 46.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 288
Crystal growth procedure: 300mM Ammonium citrate, 24% PEG 3350
Matthews coefficient: 3.45
Solvent content (%): 64.33
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: 2022-09-14
Lon protease proteolytic domain (PDB entry 6WZV)
Macromolecule: Lon protease homolog, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.53
Sequence length: 218 residues
Sequence: MGSDKIHHHHHHERMYDVTPPGVVMGLAWTAMGGSTLFVETSLRRPQDKDAKGDKDGSLEVTGQLGEVMKESARIAYTFARAFLMQHAPANDYLVTSHIHLHVPEGATPKDGPSAGCTIVTALLSLAMGRPVRQNLAMTGEVSLTGKILPVGGIKEKTIAAKRAGVTCIVLPAENKKDFYDLAAFITEGLEVHFVEHYREIFDIAFPDEQAEALAVER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.1768
R free: 0.2139
Average B factor: 69.4967
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 1.6M ammonium sulfate, 0.1M Bicine
Matthews coefficient: 3.74
Solvent content (%): 67.08
Ligand: N-[(1R)-1-borono-3-methylbutyl]-Nalpha-(pyrazine-2-carbonyl)-D-phenylalaninamide (UFY)
Ligand formula: C19 H25 B N4 O4
Ligand molecular weight: 384.237
Ligand SMILES: B(C(CC(C)C)NC(=O)C(Cc1ccccc1)NC(=O)c2cnccn2)(O)O
Ligand InChI: InChI=1S/C19H25BN4O4/c1-13(2)10-17(20(27)28)24-18(25)15(11-14-6-4-3-5-7-14)23-19(26)16-12-21-8-9-22-16/h3-9,12-13,15,17,27-28H,10-11H2,1-2H3,(H,23,26)(H,24,25)/t15-,17+/m1/s1
Release date: 2021-04-14
X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and Muc5AC-3,13 (PDB entry 8UJF)
Macromolecule: Glycosyl transferase
Type: Protein, polypeptide(L)
Source organism: Toxoplasma gondii ME49
EC number: 2.4.1.41
Sequence length: 563 residues
Sequence: GARDVQEGVSSFEESGGAQLPPRVHALEVLEGAGPGRLHGRLGIKPDGQPGYTRAPSPPTDLSMPQALARGGGFNLYLSDHLELDRTAPDARHASCRQLHYDLSTLPKASVIIVFYNEPFSTLMRSVHSVLNGTPPQILEELILVDDGSTLPYIREDGNQQLVEYLKLLPAKVRLIRNEVRKGIVGARMKGIRASRAPIFAILDSHIEVSPQWLEPLLLRIKEDSRRVVMPQIDGIDAETFKHIAGGIGCKLGFLWKLMEHSYEGHQTARLPPEERQPSPTDFQTSPAMAGGLFAANKAFFFDVGAYDEDFQFWGTENLELSFRLWQCGGVLECAPCSRVYHIFRKGGSGYSSPGDSITINKMRTMLWMDEYADLAWRVIGKPRVNYRPESLEKRREWRKRKGCKSFRWFMENVFPEGDVVTLDDVPYLGPLRNDKIGMCLDNMGWASPGHAVGLEYCHGGDTQTFMFFRKVGHVMPVNDDEACLQPSGRLDWCRGTAQFWWDFTSSGQLMFRETKQCLSAFGRKLRMVECDDTDPYQIWSWTAYNPPDTFTFPSVSRSIRSG
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.87
R work: 0.2173
R free: 0.2741
Average B factor: 51.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v)
Matthews coefficient: 2.7
Solvent content (%): 54.53
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: 2024-05-15
MEK1 in complex with compound 4 (PDB entry 7B7R)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1,Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 326 residues
Sequence: MAHHHHHHAAAENLYFQLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIGSGSGSMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.194
R free: 0.218
Average B factor: 36.62
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Crystals were obtained from hanging drops by mixing a 1:1 ratio of protein solution with well solution containing 2 M AmSO4, 0.1 M NaCl and 0.1 M Bis-tris pH 6.1-6.2
Matthews coefficient: 2.23
Solvent content (%): 44.8
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2021-03-03
Histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 2-(1H-pyrazol-3-yl)isonicotinic acid (PDB entry 7DYG)
Macromolecule: Lysine-specific demethylase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.66
Sequence length: 330 residues
Sequence: AQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1609
R free: 0.1857
Average B factor: 27.7658
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.2M potassium citrate tribasic monohydrate PH 8.3, 20% w/v PEG 3350
Matthews coefficient: 2.55
Solvent content (%): 51.82
Ligand: 2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid (0WS)
Ligand formula: C9 H7 N3 O2
Ligand molecular weight: 189.171
Ligand SMILES: c1c[nH]nc1c2cc(ccn2)C(=O)O
Ligand InChI: InChI=1S/C9H7N3O2/c13-9(14)6-1-3-10-8(5-6)7-2-4-11-12-7/h1-5H,(H,11,12)(H,13,14)
Release date: 2022-01-26
Crystal structure of human KRAS G12C covalently bound with AstraZeneca WO2020/178282A1 compound 76 (PDB entry 8DNJ)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 184 residues
Sequence: MKHHHHHHHLVPRGSMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.2392
R free: 0.2889
Average B factor: 25.834
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.001M MgCl2, 0.1 M MES pH 6.5, 30% PEG 4000,  10% Ethanol
Matthews coefficient: 1.91
Solvent content (%): 35.58
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: 2022-08-17
APE1 Y269A product complex with abasic DNA (PDB entry 6W4I)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTAMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1851
R free: 0.2268
Average B factor: 37.63
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 24% PEG 3350, 0.1 M Bis Tris Propane (pH 6.5), 0.2 M Sodium Fluoride
Matthews coefficient: 3.04
Solvent content (%): 59.58
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: 2020-06-17
NEDD4 HECT with covalently bound indole-based inhibitor (PDB entry 5C91)
Macromolecule: E3 ubiquitin-protein ligase NEDD4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 375 residues
Sequence: SRDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLWIEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFKFIGRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTELDLRFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEGFFELIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLMMDSEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLPPYESFEELWDKLQMAIENT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2478
R free: 0.2977
Average B factor: 50.376
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, 35 mM calcium chloride, 5 mM TCEP, 6% PEG400
Matthews coefficient: 2.29
Solvent content (%): 46.18
Ligand: methyl (2E)-4-{[(5-methoxy-1,2-dimethyl-1H-indol-3-yl)carbonyl]amino}but-2-enoate (4YU)
Ligand formula: C17 H20 N2 O4
Ligand molecular weight: 316.352
Ligand SMILES: Cc1c(c2cc(ccc2n1C)OC)C(=O)NCC=CC(=O)OC
Ligand InChI: InChI=1S/C17H20N2O4/c1-11-16(17(21)18-9-5-6-15(20)23-4)13-10-12(22-3)7-8-14(13)19(11)2/h5-8,10H,9H2,1-4H3,(H,18,21)
Release date: 2015-09-30
Crystal structure of human Casein Kinase I delta in complex with compound 31a (PDB entry 6F1W)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 314 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.864
R work: 0.1809
R free: 0.2064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 5.5, 10 % (w/v) PEG 4000, 0.2 M lithium sulfate
Matthews coefficient: 2.54
Solvent content (%): 51.58
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: 2019-03-13
Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 (PDB entry 6J8N)
Macromolecule: Small vasohibin-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 66 residues
Sequence: MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQMQPPGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1853
R free: 0.2102
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000
Matthews coefficient: 2.77
Solvent content (%): 55.57
Release date: 2019-06-19