satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of KDM4D with tetrazolhydrazide compound 5 (PDB entry 6ETE)
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): 1.468
R work: 0.1276
R free: 0.1534
Average B factor: 27.331
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 (%): 51.42
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
Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C) (PDB entry 6ZKZ)
Macromolecule: HLA class I histocompatibility antigen, alpha chain E
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 276 residues
Sequence: GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQCAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.22361
R free: 0.26731
Average B factor: 55.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Tris pH 8.5, 20% (w/v) PEG 4000, 15% Glycerol
Matthews coefficient: 2.42
Solvent content (%): 49.14
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: 2022-01-26
KRAS4b WT 1-185 bound to GDP-Mg2+ (PDB entry 8ECR)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.1471
R free: 0.1688
Average B factor: 24.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% PEG8000, 200 mM Magnesium chloride, 100 mM Tris-HCl pH 8.5
Matthews coefficient: 2.15
Solvent content (%): 42.92
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: 2023-09-06
Crystal structure of the b'-a' domain of oxidized protein disulfide isomerase complexed with alpha-synuclein peptide (31-41) (PDB entry 5CRW)
Macromolecule: Protein disulfide-isomerase
Type: Protein, polypeptide(L)
Source organism: Humicola insolens
EC number: 5.3.4.1
Sequence length: 247 residues
Sequence: GPLGSPLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.184
R free: 0.217
Average B factor: 27.1
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% (w/v) PEG 3350, 0.1 M HEPES buffer (pH 7.5)
Matthews coefficient: 2.19
Solvent content (%): 43.8
Release date: 2015-09-09
HUMAN CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5-BROMOBENZOTRIAZOLE (PDB entry 6TLV)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 399 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.1444
R free: 0.1726
Average B factor: 34.744
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M sodium HEPES/MOPS buffer pH 7.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20000
Matthews coefficient: 2.73
Solvent content (%): 54.92
Ligand: 6-bromanyl-1~{H}-benzotriazole (NKW)
Ligand formula: C6 H4 Br N3
Ligand molecular weight: 198.02
Ligand SMILES: c1cc2c(cc1Br)[nH]nn2
Ligand InChI: InChI=1S/C6H4BrN3/c7-4-1-2-5-6(3-4)9-10-8-5/h1-3H,(H,8,9,10)
Release date: 2020-12-16
Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor (PDB entry 6EMH)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 367 residues
Sequence: GGSMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Bis-Tris pH5.5, 200 mM NaCl, 29% PEG 3350, 1mM AMP-PCP, 0.4 mM Zwittergent 3-14, 10% Ethylene glycol
Matthews coefficient: 2.36
Solvent content (%): 47.91
Ligand: BETA-MERCAPTOETHANOL (BME)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: C(CS)O
Ligand InChI: InChI=1S/C2H6OS/c3-1-2-4/h3-4H,1-2H2
Release date: 2018-08-08
The STK17A (DRAK1) Kinase Domain Bound to CKJB68 (PDB entry 7QUE)
Macromolecule: Serine/threonine-protein kinase 17A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 275 residues
Sequence: SMVRTEPFQDGYSLCPGRELGRGKFAVVRKCIKKDSGKEFAAKFMRKRRKGQDCRMEIIHEIAVLELAQDNPWVINLHEVYETASEMILVLEYAAGGEIFDQCVADREEAFKEKDVQRLMRQILEGVHFLHTRDVVHLDLKPQNILLTSESPLGDIKIVDFGLSRILKNSEELREIMGTPEYVAPEILSYDPISMATDMWSIGVLTYVMLTGISPFLGNDKQETFLNISQMNLSYSEEEFDVLSESAVDFIRTLLVKKPEDRATAEECLKHPWLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2336
R free: 0.2664
Average B factor: 70.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 19% PEG3350, 0.3 M ammonium formate
Matthews coefficient: 2.77
Solvent content (%): 55.54
Ligand: ~{N}-(phenylmethyl)-7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxamide (F7I)
Ligand formula: C24 H23 N5 O3
Ligand molecular weight: 429.471
Ligand SMILES: c1ccc(cc1)CNC(=O)c2ccc-3cc2OCCOCCNc4ccn5c(c3cn5)n4
Ligand InChI: InChI=1S/C24H23N5O3/c30-24(26-15-17-4-2-1-3-5-17)19-7-6-18-14-21(19)32-13-12-31-11-9-25-22-8-10-29-23(28-22)20(18)16-27-29/h1-8,10,14,16H,9,11-13,15H2,(H,25,28)(H,26,30)
Release date: 2022-02-02
Crystal structure of c-MET bound by compound 2 (PDB entry 7B3T)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.211
R free: 0.261
Average B factor: 62.99
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 273
Crystal growth procedure: 25 % PEG8000, 0.2 M Li2SO4
Matthews coefficient: 2.55
Solvent content (%): 51.75
Ligand: 3-(phenylmethyl)-1~{H}-pyrrolo[2,3-b]pyridine (SVK)
Ligand formula: C14 H12 N2
Ligand molecular weight: 208.258
Ligand SMILES: c1ccc(cc1)Cc2c[nH]c3c2cccn3
Ligand InChI: InChI=1S/C14H12N2/c1-2-5-11(6-3-1)9-12-10-16-14-13(12)7-4-8-15-14/h1-8,10H,9H2,(H,15,16)
Release date: 2020-12-09
KRAS-G12C in complex with BI-2865 (PDB entry 8AZX)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.04
R work: 0.1611
R free: 0.197
Average B factor: 21.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2mM Magnesium Chloride, 20% PEG 2000, 100mM sodium acetate pH 4.4
Matthews coefficient: 2.54
Solvent content (%): 51.64
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2023-06-07
Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose (PDB entry 6ZFN)
Macromolecule: Glycoprotein endo-alpha-1,2-mannosidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.130
Sequence length: 382 residues
Sequence: MNHKVHHHHHHIEGRHMPLNNYLHVFYYSWYGNPQFDGKYIHWNHPVLEHWDPRIAKNYPQGRHNPPDDIGSSFYPELGSYSSRDPSVIETHMRQMRSASIGVLALSWYPPDVNDENGEPTDNLVPTILDKAHKYNLKVTFHIEPYSNRDDQNMYKNVKYIIDKYGNHPAFYRYKTKTGNALPMFYVYDSYITKPEKWANLLTTSGSRSIRNSPYDGLFIALLVEEKHKYDILQSGFDGIYTYFATNGFTYGSSHQNWASLKLFCDKYNLIFIPSVGPGYIDTSIRPWNTQNTRNRINGKYYEIGLSAALQTRPSLISITSFNQWHEGTQIEKAVPKRTSNTVYLDYRPHKPGLYLELTRKWSEKYSKERATYALDRQLPVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1063
R free: 0.1279
Average B factor: 14.999
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 279
Crystal growth procedure: 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 12.8% PEG-MME 2000.
Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.3 mM GlcMan4OMe (10 x molar ratio). 500 nl protein solution and 500 nl reservoir solution.
Matthews coefficient: 2.07
Solvent content (%): 40.5
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: 2020-11-18
Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK204 (PDB entry 5LIY)
Macromolecule: Aldo-keto reductase family 1 member B10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 316 residues
Sequence: MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDLFPRDDKGNAIGGKATFLDAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTAYSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDFKLSDEEMATILSFNRNWRACNLLQSSHLEDYPFNAEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1813
R free: 0.2216
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 100 mM sodium cacodylate
Matthews coefficient: 2.48
Solvent content (%): 50.43
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2016-10-12
Irak4-inhibitor co-structure (PDB entry 4ZTN)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.2089
R free: 0.2243
Average B factor: 64.93
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 289
Crystal growth procedure: 1.80 to 2.0 M Sodium Malonate, 0.2 M Sodium Acetate, 25 mM Hexamminecobalt(III)chloride, 0.05%w/v Pluronic-F-68
Matthews coefficient: 2.62
Solvent content (%): 53.01
Ligand: 5-(1,3-benzothiazol-2-yl)-2-(morpholin-4-yl)-6-[(3R)-piperidin-3-ylamino]pyrimidin-4(3H)-one (4S3)
Ligand formula: C20 H24 N6 O2 S
Ligand molecular weight: 412.509
Ligand SMILES: c1ccc2c(c1)nc(s2)C3=C(N=C(NC3=O)N4CCOCC4)NC5CCCNC5
Ligand InChI: InChI=1S/C20H24N6O2S/c27-18-16(19-23-14-5-1-2-6-15(14)29-19)17(22-13-4-3-7-21-12-13)24-20(25-18)26-8-10-28-11-9-26/h1-2,5-6,13,21H,3-4,7-12H2,(H2,22,24,25,27)/t13-/m1/s1
Release date: 2015-09-02
Crystal structure of EGFR_DMX in complex with covalently bound fragment 4 (PDB entry 8HV3)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.21202
R free: 0.24993
Average B factor: 44.518
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Matthews coefficient: 3.39
Solvent content (%): 63.67
Ligand: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL (PE5)
Ligand formula: C18 H38 O9
Ligand molecular weight: 398.489
Ligand SMILES: CCOCCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C18H38O9/c1-2-20-5-6-22-9-10-24-13-14-26-17-18-27-16-15-25-12-11-23-8-7-21-4-3-19/h19H,2-18H2,1H3
Release date: 2023-12-13
Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon Polypeptide, alternative C-terminus (PDB entry 8F13)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 95 residues
Sequence: SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1744
R free: 0.2078
Average B factor: 29.8097
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Potassium sodium tartrate, 0.1 M tri-Sodium citrate pH 5.6, 2.0 M Ammonium sulfate
Matthews coefficient: 2.95
Solvent content (%): 58.3
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: 2023-02-15
Post-catalytic nicked complex of DNA Polymerase Lambda with bound mismatched DSB substrate (PDB entry 7M0C)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 346 residues
Sequence: GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1804
R free: 0.2286
Average B factor: 31.27
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG 8000, 13.5% (v/v) glycerol, 0.2M NDSB-201
Matthews coefficient: 3.03
Solvent content (%): 59.4
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: 2022-03-16
The co-crystal structure of DYRK2 with a small molecule inhibitor 7 (PDB entry 7DH9)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 324 residues
Sequence: HDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.194
R work: 0.1879
R free: 0.2176
Average B factor: 37.0451
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 0.01 M sodium borate, pH 7.5-9.5
Matthews coefficient: 3.65
Solvent content (%): 66.27
Ligand: [2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridin-4-yl]methanol (H7F)
Ligand formula: C22 H26 N2 O3 S
Ligand molecular weight: 398.518
Ligand SMILES: COc1ccc2c(c1)c(c3cc(cc(c3n2)CO)OC)SCC4CCNCC4
Ligand InChI: InChI=1S/C22H26N2O3S/c1-26-16-3-4-20-18(10-16)22(28-13-14-5-7-23-8-6-14)19-11-17(27-2)9-15(12-25)21(19)24-20/h3-4,9-11,14,23,25H,5-8,12-13H2,1-2H3
Release date: 2021-11-17
Domain II of the human copper chaperone in complex with human Cu,Zn superoxide dismutase (PDB entry 6FOL)
Macromolecule: Copper chaperone for superoxide dismutase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 150 residues
Sequence: GANLGAAVAILGGPGTVQGVVRFLQLTPERCLIEGTIDGLEPGLHGLHVHQYGDLTNNCNSCGNHFNPDGASHGGPQDSDRHRGDLGNVRADADGRAIFRMEDEQLKVWDVIGRSLIIDEGEDDLGRGGHPLSKITGNSGERLACGIIAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.208
R free: 0.2482
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% (w/v) PEG 1500 and 0.1 M PCTP buffer pH 7.0 (sodium propionate, sodium cacodylate, and BIS-TRIS propane in the molar ratios 2:1:2, respectively)
Matthews coefficient: 4.15
Solvent content (%): 70.38
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: 2019-01-30
Crystal structure of the human METTL3-METTL14 complex with compound UOZ004 (PDB entry 7NHI)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1981
R free: 0.2218
Average B factor: 35.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.15
Solvent content (%): 42.89
Ligand: (R)-N-((3-hydroxy-1-(6-(methylamino)pyrimidin-4-yl)piperidin-3-yl)methyl)-4-((4-methylpiperidin-1-yl)methyl)benzamide (UE2)
Ligand formula: C26 H38 N6 O2
Ligand molecular weight: 466.619
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(cc2)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NC)O)C
Ligand InChI: InChI=1S/C26H38N6O2/c1-25(2)10-13-31(14-11-25)16-20-5-7-21(8-6-20)24(33)28-17-26(34)9-4-12-32(18-26)23-15-22(27-3)29-19-30-23/h5-8,15,19,34H,4,9-14,16-18H2,1-3H3,(H,28,33)(H,27,29,30)/t26-/m1/s1
Release date: 2021-09-01
Crystal structure of chimeric carbonic anhydrase XII with inhibitor (PDB entry 4Q08)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVEFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDAGKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.07
R work: 0.128
R free: 0.156
Average B factor: 14.485
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 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, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 1.99
Solvent content (%): 37.7
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2015-01-28