satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the human METTL3-METTL14 complex bound to Compound 5 (ASI_M3M_051) (PDB entry 6TTX)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 580 residues
Sequence: MSDTWSSIQAHKKQLDSLRERLQRRRKQDSGHLDLRNPEAALSPTFRSDSPVPTAPTSGGPKPSTASAVPELATDPELEKKLLHHLSDLALTLPTDAVSICLAISTPDAPATQDGVESLLQKFAAQELIEVKRGLLQDDAHPTLVTYADHSKLSAMMGAVAEKKGPGEVAGTVTGQKRRAEQDSTTVAAFASSLVSGLNSSASEPAKEPAKKSRKHAASDVDLEIESLLNQQSTKEQQSKKVSQEILELLNTTTAKEQSIVEKFRSRGRAQVQEFCDYGTKEECMKASDADRPCRKLHFRRIINKHTDESLGDCSFLNTCFHMDTCKYVHYEIDACMDSEAPGSKDHTPSQELALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1914
R free: 0.2173
Average B factor: 36.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 25% PEG 3350, 200 mM Magnesium acetate
Ligand: (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)-~{N}-(piperidin-4-ylmethyl)oxolane-2-carboxamide (NX8)
Ligand formula: C16 H23 N7 O4
Ligand molecular weight: 377.398
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)C(=O)NCC4CCNCC4)O)O)N
Ligand InChI: InChI=1S/C16H23N7O4/c17-13-9-14(21-6-20-13)23(7-22-9)16-11(25)10(24)12(27-16)15(26)19-5-8-1-3-18-4-2-8/h6-8,10-12,16,18,24-25H,1-5H2,(H,19,26)(H2,17,20,21)/t10-,11+,12-,16+/m0/s1
Release date: 2020-03-04
Structure of the human JAK1 kinase domain with compound 39 (PDB entry 6N7A)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 304 residues
Sequence: GSGDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.192
R free: 0.207
Average B factor: 19.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M MES pH 5-6 and 25-35% PEG 6000
Matthews coefficient: 2.38
Solvent content (%): 48.38
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: 2019-04-24
Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser) (PDB entry 7BMI)
Macromolecule: Aspartyl/asparaginyl beta-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.16
Sequence length: 429 residues
Sequence: KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.189
R free: 0.2203
Average B factor: 48.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM HEPES sodium, 200 mM ammonium chloride, 20% w/v PEG 4000, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein
Matthews coefficient: 2.59
Solvent content (%): 52.6
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: 2021-06-02
The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of PTEN (PDB entry 7PC7)
Macromolecule: Gamma-1-syntrophin,Annexin A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 414 residues
Sequence: GSHMGGERTVTIRRQTVGGFGLSIKGGAEHNIPVVVSKISKEQRAELSGLLFIGDAILQINGINVRKCRHEEVVQVLRNAGEEVTLTVSFLKRAPGSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1852
R free: 0.2183
Average B factor: 56.4524
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris 8.5,  22 % v/v PEG Smear Broad
Matthews coefficient: 2.86
Solvent content (%): 57.06
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: 2022-04-20
Crystal Structure of EGFR-T790M/V948R in Complex with Mavelertinib and EAI001 (PDB entry 6Z4D)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1931
R free: 0.2214
Average B factor: 52.2716
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 27.5 % PEG3350, 100 mM MgSO4, 2 % ethylen glycole, 5.0 mg/mL EGFR-T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)
Solvent content (%): 34.9
Ligand: N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-methyl-9H-purin-2-yl}pyrrolidin-3-yl]propanamide (8BS)
Ligand formula: C18 H24 F N9 O2
Ligand molecular weight: 417.441
Ligand SMILES: CCC(=O)NC1CN(CC1F)c2nc(c3c(n2)n(cn3)C)Nc4cn(nc4OC)C
Ligand InChI: InChI=1S/C18H24FN9O2/c1-5-13(29)21-11-8-28(6-10(11)19)18-23-15(14-16(24-18)26(2)9-20-14)22-12-7-27(3)25-17(12)30-4/h7,9-11H,5-6,8H2,1-4H3,(H,21,29)(H,22,23,24)/t10-,11-/m1/s1
Release date: 2020-11-11
X-ray structure of the haloalkane dehalogenase HaloTag7 with an insertion of Calmodulin-M13 fusion at position 154-156 that mimic the structure of CaProLa, an calcium gated protein labeling technology (PDB entry 8B6Q)
Macromolecule: Haloalkane dehalogenase,Calmodulin-1,Haloalkane dehalogenase,Calmodulin-1,M13 peptide
Type: Protein, polypeptide(L)
Source organism: Rhodococcus sp. (in: high G+C Gram-positive bacteria)
EC number: 3.8.1.5
Sequence length: 472 residues
Sequence: GIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRTTGSDQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVVMMTAGGTGGDSSRRKFNKTGKALRAIGRLSSLEGGSVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTLEI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2806
R free: 0.3182
Average B factor: 89.43
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.0, 0.2 M calcium acetate, 18% (m/v) PEG 8000
Matthews coefficient: 2.33
Solvent content (%): 47.27
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2023-10-11
Crystal structure of the human CDKL5 kinase domain with compound YL-354 (PDB entry 8CIE)
Macromolecule: Cyclin-dependent kinase-like 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 304 residues
Sequence: SMKIPNIGNVMNKFEILGVVGEGAYGVVLKCRHKETHEIVAIKKFKDSEENEEVKETTLRELKMLRTLKQENIVELKEAFRRRGKLYLVFEYVEKNMLELLEEMPNGVPPEKVKSYIYQLIKAIHWCHKNDIVHRDIKPENLLISHNDVLKLCDFGFARNLSEGNNANYDEEVATRWYRSPELLLGAPYGKSVDMWSVGCILGELSDGQPLFPGESEIDQLFTIQKVLGPLPSEQMKLFYSNPRFHGLRFPAVNHPQSLERRYLGILNSVLLDLMKNLLKLDPADRYLTEQCLNHPTFQTQRLL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2876
R free: 0.3098
Average B factor: 58.18
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M tri-sodium citrate, 1.1 M lithium sulfate, 0.4 M ammonium sulfate
Matthews coefficient: 2.12
Solvent content (%): 41.91
Ligand: 4-[[3,5-bis(fluoranyl)phenyl]carbonylamino]-~{N}-piperidin-4-yl-1~{H}-pyrazole-3-carboxamide (US0)
Ligand formula: C16 H17 F2 N5 O2
Ligand molecular weight: 349.335
Ligand SMILES: c1c(cc(cc1F)F)C(=O)Nc2c[nH]nc2C(=O)NC3CCNCC3
Ligand InChI: InChI=1S/C16H17F2N5O2/c17-10-5-9(6-11(18)7-10)15(24)22-13-8-20-23-14(13)16(25)21-12-1-3-19-4-2-12/h5-8,12,19H,1-4H2,(H,20,23)(H,21,25)(H,22,24)
Release date: 2023-06-14
Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7Guanine (PDB entry 7ZEH)
Macromolecule: 7-methylguanosine phosphate-specific 5'-nucleotidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.91
Sequence length: 302 residues
Sequence: RSMAEEVSTLMKATVLMRQPGRVQEIVGALRKGGGDRLQVISDFDMTLSRFAYNGKRCPSSYNILDNSKIISEECRKELTALLHHYYPIEIDPHRTVKEKLPHMVEWWTKAHNLLCQQKIQKFQIAQVVRESNAMLREGYKTFFNTLYHNNIPLFIFSAGIGDILEEIIRQMKVFHPNIHIVSNYMDFNEDGFLQGFKGQLIHTYNKNSSACENSGYFQQLEGKTNVILLGDSIGDLTMADGVPGVQNILKIGFLNDKVEERRERYMDSYDIVLEKDETLDVVNGLLQHILCQGVQLEMQGP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1877
R free: 0.2199
Average B factor: 28.74
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.6
Crystallization temperature (K): 292.15
Crystal growth procedure: 5 % PEG 400, 1.73 M ammonium sulfate, 0.1 M MES pH 5.6
Matthews coefficient: 2.6
Solvent content (%): 52.71
Ligand: N7-(3,4-difluorobenzyl) guanine (IPQ)
Ligand formula: C12 H10 F2 N5 O
Ligand molecular weight: 278.238
Ligand SMILES: c1cc(c(cc1C[n+]2c[nH]c3c2c(nc(n3)N)O)F)F
Ligand InChI: InChI=1S/C12H9F2N5O/c13-7-2-1-6(3-8(7)14)4-19-5-16-10-9(19)11(20)18-12(15)17-10/h1-3,5H,4H2,(H3,15,17,18,20)/p+1
Release date: 2022-05-25
FACTOR VIIA IN COMPLEX WITH THE INHIBITOR 4-BROMO-2-METHOXYPHENOL (PDB entry 4X8S)
Macromolecule: Factor VIIa (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): 2.1
R work: 0.1755
R free: 0.199
Average B factor: 33.31
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: 3.83
Solvent content (%): 67.92
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: 2015-03-25
Co-crystal structure of LMW-PTP in complex with 2-(benzothiazol-2-ylamino)-2-oxo-1-phenylethanesulfonic acid (PDB entry 5KQG)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 178 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAEQATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1672
R free: 0.1941
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25-30% PEGME 5000, 100 mM Bis-Tris, pH 6.0-6.5
Matthews coefficient: 2.26
Solvent content (%): 45.53
Ligand: (1~{S})-2-(1,3-benzothiazol-2-ylamino)-2-oxidanylidene-1-phenyl-ethanesulfonic acid (6VX)
Ligand formula: C15 H12 N2 O4 S2
Ligand molecular weight: 348.397
Ligand SMILES: c1ccc(cc1)C(C(=O)Nc2nc3ccccc3s2)S(=O)(=O)O
Ligand InChI: InChI=1S/C15H12N2O4S2/c18-14(13(23(19,20)21)10-6-2-1-3-7-10)17-15-16-11-8-4-5-9-12(11)22-15/h1-9,13H,(H,16,17,18)(H,19,20,21)/t13-/m0/s1
Release date: 2016-10-12
Crystal structure of MYST acetyltransferase domain in complex with inhibitor 34 (PDB entry 6OIP)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 273 residues
Sequence: VKYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSWVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1847
R free: 0.2219
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 20% PEG 3350, 0.2 M K/Na Tartrate
Matthews coefficient: 2.51
Solvent content (%): 51
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: 2019-07-03
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5ORO)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.2204
R free: 0.2808
Average B factor: 59.6358
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350
Matthews coefficient: 2.8
Solvent content (%): 55.99
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: 2017-11-01
Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mg2+ for 600s (PDB entry 5KFP)
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): 1.7
R work: 0.1769
R free: 0.2209
Average B factor: 29.1675
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.2
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2016-06-22
Structure of human deoxyhypusine hydroxylase (PDB entry 4D50)
Macromolecule: DEOXYHYPUSINE HYDROXYLASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.29
Sequence length: 294 residues
Sequence: GPLGSMVTEQEVDAIGQTLVDPKQPLQARFRALFTLRGLGGPGAIAWISQAFDDDSALLKHELAYCLGQMQDARAIPMLVDVLQDTRQEPMVRHEAGEALGAIGDPEVLEILKQYSSDPVIEVAETCQLAVRRLEWLQQHGGEPAAGPYLSVDPAPPAEERDVGRLREALLDESRPLFERYRAMFALRNAGGEEAALALAEGLHCGSALFRHEVGYVLGQLQHEAAVPQLAAALARCTENPMVRHECAEALGAIARPACLAALQAHADDPERVVRESCEVALDMYEHETGRAFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.20261
R free: 0.2465
Average B factor: 18.899
Crystallization pH: 7.2
Crystal growth procedure: 30% POLYETHYLENE GLYCOL 6000 (W/V), 100 MM BIS-TRIS PROPANE PH 7.2 - 7.4, 400 MM GUANIDINE CHLORIDE
Matthews coefficient: 2.14
Solvent content (%): 42
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2015-04-15
Crystal structure of pathogenic mutants of human mitochodnrial PheRS (PDB entry 5MGH)
Macromolecule: Phenylalanine--tRNA ligase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.20
Sequence length: 405 residues
Sequence: PGSVVELLGKSYPQDDHSNLTRKVLTRVGRNLHNQQHHALWLIKERVKEHFYKQYVGRFGTPLFSVYDNLSPVVTTWQNFDSLLIPADHPSRKKGDNYYLNRTHMLRAHTSAHQWDLLHAGLDAFLVVGDVYRRDQIDSQHYPIFHQLEAVRLFSKHELFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVEFDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGEWLEVLGCGVMEQQLVNSAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSENYAENDFYDLVRTIGGDLVEKVDLIDKFVHPKTHKTSHCYRITYRHMERTLSQREVRHIHQALQEAAVQLLGVEGRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1976
R free: 0.2299
Average B factor: 42.6683
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 2 mM DTT, 100 mM bis-Tris propane pH 7 and 1.8 M sodium acetate pH 7
Matthews coefficient: 2.52
Solvent content (%): 51.19
Ligand: PHENYLALANINE (PHE)
Ligand formula: C9 H11 N O2
Ligand molecular weight: 165.189
Ligand SMILES: c1ccc(cc1)CC(C(=O)O)N
Ligand InChI: InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1
Release date: 2017-05-03
Crystal structure of CLK3 in complex with CX-4945 (PDB entry 6KHF)
Macromolecule: Dual specificity protein kinase CLK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 490 residues
Sequence: MHHCKRYRSPEPDPYLSYRWKRRRSYSREHEGRLRYPSRREPPPRRSRSRSHDRLPYQRRYRERRDSDTYRCEERSPSFGEDYYGPSRSRHRRRSRERGPYRTRKHAHHCHKRRTRSCSSASSRSQQSSKRSSRSVEDDKEGHLVCRIGDWLQEDYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHTSRNPSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.598
R work: 0.2234
R free: 0.2837
Average B factor: 49.9642
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 60% (v/v) Tacsimate pH 7.0, 0.025% dichloromethane
Matthews coefficient: 2.4
Solvent content (%): 48.65
Ligand: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid (3NG)
Ligand formula: C19 H12 Cl N3 O2
Ligand molecular weight: 349.77
Ligand SMILES: c1cc(cc(c1)Cl)Nc2c3ccncc3c4ccc(cc4n2)C(=O)O
Ligand InChI: InChI=1S/C19H12ClN3O2/c20-12-2-1-3-13(9-12)22-18-15-6-7-21-10-16(15)14-5-4-11(19(24)25)8-17(14)23-18/h1-10H,(H,22,23)(H,24,25)
Release date: 2019-10-02
Human VKOR with phenindione (PDB entry 6WV6)
Macromolecule: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
Type: Protein, polypeptide(L)
Source organism: Aequorea victoria
EC number: 1.17.4.4
Sequence length: 390 residues
Sequence: MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQENSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2261
R free: 0.2678
Average B factor: 50.9532
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 34% PEG400, 80 mM lithium sulfate, 0.1 M MES, pH 6.5
Matthews coefficient: 3.17
Solvent content (%): 61.17
Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (OLC)
Ligand formula: C21 H40 O4
Ligand molecular weight: 356.54
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)OCC(CO)O
Ligand InChI: InChI=1S/C21H40O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h9-10,20,22-23H,2-8,11-19H2,1H3/b10-9-/t20-/m1/s1
Release date: 2020-11-11
Crystal structure of human Carbonic anhydrase II in complex with (R)-4-(3-(1-(6-nitropyridin-2-yl)pyrrolidin-3-yl)thioureido)benzenesulfonamide (PDB entry 8BJX)
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): 1.283
R work: 0.1562
R free: 0.2033
Average B factor: 18.559
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.07
Solvent content (%): 40.45
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: 2023-11-22