satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of p38alpha in complex with a photoswitchable 2-Azothiazol-based Inhibitor (compound 2) (PDB entry 6HWU)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 362 residues
Sequence: GSHSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1905
R free: 0.2466
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES pH 5.6-6.2, 20-30 % PEG4000, 40mM BOG
Matthews coefficient: 2.32
Solvent content (%): 46.92
Ligand: octyl beta-D-glucopyranoside (BOG)
Ligand formula: C14 H28 O6
Ligand molecular weight: 292.369
Ligand SMILES: CCCCCCCCOC1C(C(C(C(O1)CO)O)O)O
Ligand InChI: InChI=1S/C14H28O6/c1-2-3-4-5-6-7-8-19-14-13(18)12(17)11(16)10(9-15)20-14/h10-18H,2-9H2,1H3/t10-,11-,12+,13-,14-/m1/s1
Release date: 2019-04-17
Crystal Structure of the C-terminal Guanine Nucleotide Exchange Factor Module of Human Trio (PDB entry 6D8Z)
Macromolecule: Triple functional domain protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 319 residues
Sequence: GEFEERKSSSLKRRHYVLQELVETERDYVRDLGYVVEGYMALMKEDGVPDDMKGKDKIVFGNIHQIYDWHRDFFLGELEKCLEDPEKLGSLFVKHERRLHMYIAYCQNKPKSEHIVSEYIDTFFEDLKQRLGHRLQLTDLLIKPVQRIMKYQLLLKDFLKYSKKASLDTSELERAVEVMCIVPRRCNDMMNVGRLQGFDGKIVAQGKLLLQDTFLVTDQDAGLLPRCRERRIFLFEQIVIFSEPLDKKKGFSMPGFLFKNSIKVSCLCLEENVENDPCKFALTSRTGDVVETFILHSSSPSVRQTWIHEINQILENQRN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.225
R free: 0.266
Average B factor: 75.96
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 14% PEG 3350, 100MM HEPES PH 7.5,
 HANGING DROP, 293K, VAPOR DIFFUSION, HANGING DROP
Matthews coefficient: 2.45
Solvent content (%): 49.77
Release date: 2019-02-20
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 3-Amino-4-methyl-1,3-dihydro-2H-indol-2-one (N10042a) (PDB entry 5FYU)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.1937
R free: 0.2274
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.1
Solvent content (%): 41.44
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-03-23
Human carbonic anhydrase II in complex with troglitazone (PDB entry 7M23)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1204
R free: 0.151
Average B factor: 14.036
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 293
Crystal growth procedure: Protein concentration was 4 mg/mL; equal volumes (250 nL) of protein plus reservoir were added to the plate; the reservoir was 1.5 M tri-potassium citrate, 0.1 M tris buffer at pH 8.3.
Matthews coefficient: 2.07
Solvent content (%): 40.65
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: 2022-02-02
Crystal structure of the human METTL3-METTL14 complex with compound UOZ059b (PDB entry 7OEH)
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): 2.01
R work: 0.2025
R free: 0.2286
Average B factor: 47.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.17
Solvent content (%): 43.37
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2021-10-20
MTH1 in complex with compound 5 (PDB entry 6US2)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.80012657096
R work: 0.176010896719
R free: 0.234421783229
Average B factor: 20.3422922636
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 0.1M sodium acetate pH 4.0, 0.2M lithium sulfate
Matthews coefficient: 1.99
Solvent content (%): 38.13
Ligand: N-[5-(2,3-dimethylphenyl)-1,2,3,4-tetrahydro-1,6-naphthyridin-7-yl]acetamide (S3O)
Ligand formula: C18 H21 N3 O
Ligand molecular weight: 295.379
Ligand SMILES: Cc1cccc(c1C)c2c3c(cc(n2)NC(=O)C)NCCC3
Ligand InChI: InChI=1S/C18H21N3O/c1-11-6-4-7-14(12(11)2)18-15-8-5-9-19-16(15)10-17(21-18)20-13(3)22/h4,6-7,10,19H,5,8-9H2,1-3H3,(H,20,21,22)
Release date: 2020-04-01
Crystal structure of the vertebrate conserved region (VCR) of human METTL16 (PDB entry 6M1U)
Macromolecule: RNA N6-adenosine-methyltransferase METTL16,RNA N6-adenosine-methyltransferase METTL16
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 164 residues
Sequence: MKPITFVVLASVMKELSLKASPLRSETAEGIVVVTTWIEKILTDLKVQHKRVPCGKEEVSLFLTAIENSWIHLRRKKRERVRQLREVPRAPEDVIQALEEKKGVAGQYLFKCLINVKKEVDDALVEMHWVEGQNRDLMNQLCTYIRNQIFRLVAVNLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.791
R work: 0.2336
R free: 0.263
Average B factor: 87.7021
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris-HCl, pH 7.4, 20% (w/v) PEG3350, 200 mM sodium citrate, 4% (w/v) formamide and 5 mM dextran sulfate sodium salt.
Matthews coefficient: 2.62
Solvent content (%): 52.97
Release date: 2020-04-01
CDK8-CYCC IN COMPLEX WITH 8-(1-Methyl-2,2-dioxo-2,3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-[1,6]naphthyridine-2-carboxylic acid methylamide (PDB entry 5I5Z)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 370 residues
Sequence: DDKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.23741
R free: 0.27423
Average B factor: 42.716
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 0.2 M sodium formate, pH 6.9
Matthews coefficient: 3.1
Solvent content (%): 59.4
Ligand: N-methyl-8-(1-methyl-2,2-dioxo-2,3-dihydro-1H-2lambda~6~,1-benzothiazol-5-yl)-1,6-naphthyridine-2-carboxamide (68U)
Ligand formula: C18 H16 N4 O3 S
Ligand molecular weight: 368.41
Ligand SMILES: CNC(=O)c1ccc2cncc(c2n1)c3ccc4c(c3)CS(=O)(=O)N4C
Ligand InChI: InChI=1S/C18H16N4O3S/c1-19-18(23)15-5-3-12-8-20-9-14(17(12)21-15)11-4-6-16-13(7-11)10-26(24,25)22(16)2/h3-9H,10H2,1-2H3,(H,19,23)
Release date: 2016-04-13
Structure of G9a SET-domain with H3K9M mutant peptide and SAM (PDB entry 5T0K)
Macromolecule: Histone-lysine N-methyltransferase EHMT2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 281 residues
Sequence: NRAIRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLARLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.165
R free: 0.1928
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol
Matthews coefficient: 2.33
Solvent content (%): 47.26
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-10-05
Structure of Compound 14 bound to CK2alpha (PDB entry 8AEK)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1717
R free: 0.1983
Average B factor: 17.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.01
Solvent content (%): 38.95
Ligand: 2-[5-(trifluoromethyl)-1H-indol-3-yl]ethanenitrile (LVL)
Ligand formula: C11 H7 F3 N2
Ligand molecular weight: 224.182
Ligand SMILES: c1cc2c(cc1C(F)(F)F)c(c[nH]2)CC#N
Ligand InChI: InChI=1S/C11H7F3N2/c12-11(13,14)8-1-2-10-9(5-8)7(3-4-15)6-16-10/h1-2,5-6,16H,3H2
Release date: 2022-10-12
Crystal structure of the human RecQL4 helicase. (PDB entry 5LST)
Macromolecule: ATP-dependent DNA helicase Q4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 693 residues
Sequence: GPMAVGPEPLVPSPQPVPEVPSLDPTVLPLYSLGPSGQLAETPAEVFQALEQLGHQAFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYSRRSPCLTLVVSPLLSLMDDQVSGLPPCLKAACIHSGMTRKQRESVLQKIRAAQVHVLMLTPEALVGAGGLPPAAQLPPVAFACIDEAHCLSQWSHNFRPCYLRVCKVLRERMGVHCFLGLTATATRRTASDVAQHLAVAEEPDLHGPAPVPTNLHLSVSMDRDTDQALLTLLQGKRFQNLDSIIIYCNRREDTERIAALLRTCLHAAWVPGSGGRAPKTTAEAYHAGMCSRERRRVQRAFMQGQLRVVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAVGRAGRDGQPAHCHLFLQPQGEDLRELRRHVHADSTDFLAVKRLVQRVFPACTCTCTRPPSEQEGAVGGERPVPKYPPQEAEQLSHQAAPGPRRVCMGHERALPIQLTVQALDMPEEAIETLLCYLELHPHHWLELLATTYTHCRLNCPGGPAQLQALAHRCPPLAVCLAQQLPEDPGQGSSSVEFDMVKLVDSMGWELASVRRALCQLQWDHEPRTGVRRGTGVLVEFSELAFHLRSPGDLTAEEKDQICDFLYGRVQARERQALARLRRTFQAFHSVAFPSCGPCLEQQDEERSTRLKDLLGRYFEEEEGQEP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.1828
R free: 0.2314
Average B factor: 108.8
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293.15
Crystal growth procedure: Imidazole, Sodium formate
Matthews coefficient: 3.12
Solvent content (%): 60.62
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: 2017-07-05
HPF1 bound to catalytic fragment of PARP2 (PDB entry 6TX3)
Macromolecule: Poly [ADP-ribose] polymerase 2,Poly [ADP-ribose] polymerase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 280 residues
Sequence: MGSSHHHHHHSSGLVPRGSHPESQLDLRVQELIKLICNVQAMEEKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.96
R work: 0.2292
R free: 0.2596
Average B factor: 154.0346
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6, 25% v/v pentaerythritol propoxylate (5/4 PO/OH)
Matthews coefficient: 4.05
Solvent content (%): 69.63
Ligand: 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide (UHB)
Ligand formula: C24 H27 N9 O6
Ligand molecular weight: 537.528
Ligand SMILES: c1cc2c(c(c1)NC(=O)CN3CCN(CC3)C(=O)C4C(C(C(O4)n5cnc6c5ncnc6N)O)O)CNC2=O
Ligand InChI: InChI=1S/C24H25N9O6/c25-20-16-21(28-10-27-20)33(11-29-16)24-18(36)17(35)19(39-24)23(38)32-6-4-31(5-7-32)9-15(34)30-14-3-1-2-12-13(14)8-26-22(12)37/h1-3,8,10-11,17-19,24,35-36H,4-7,9H2,(H,26,37)(H2,25,27,28)/b30-14-/t17-,18+,19-,24+/m0/s1
Release date: 2020-02-19
Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rII) (PDB entry 5V04)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 358 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2292
R free: 0.2558
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000
Matthews coefficient: 2.6
Solvent content (%): 52.74
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-05-24
The crystal structure of CK2alpha in complex with compound 3 (PDB entry 6GMD)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.2208
R free: 0.2475
Average B factor: 25.53
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.38
Solvent content (%): 48.31
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2018-06-06
DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog (PDB entry 6MR7)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.144
R work: 0.1856
R free: 0.2516
Average B factor: 35.7238
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 50 mM imidazole pH 7.5, 16% PEG3350, and 350 mM sodium acetate
Matthews coefficient: 2.47
Solvent content (%): 50.24
Ligand: 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol (GKS)
Ligand formula: C11 H19 N4 O14 P3
Ligand molecular weight: 524.208
Ligand SMILES: C1C(OC(C1O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)CC2=C(C(=O)NC(=N2)N)NC=O
Ligand InChI: InChI=1S/C11H19N4O14P3/c12-11-14-6(9(13-4-16)10(18)15-11)1-5-2-7(17)8(27-5)3-26-31(22,23)29-32(24,25)28-30(19,20)21/h4-5,7-8,17H,1-3H2,(H,13,16)(H,22,23)(H,24,25)(H2,19,20,21)(H3,12,14,15,18)/t5-,7-,8+/m0/s1
Release date: 2019-01-30
DISEASE LINKED MUTATION IN FGFR (PDB entry 5FLF)
Macromolecule: FIBROBLAST GROWTH FACTOR RECEPTOR 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 310 residues
Sequence: MVAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDGIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.1937
R free: 0.2545
Crystallization pH: 7.5
Crystal growth procedure: 20 PEG 400, 0.75 M AMMONIUM SULPHATE, 0.1 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5
Matthews coefficient: 2.7
Solvent content (%): 54.6
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2016-03-30
Crystal structure of STAMBPL1 in complex with an engineered binder (PDB entry 7L97)
Macromolecule: AMSH-like protease
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19
Sequence length: 175 residues
Sequence: GVEGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSACKKKGFHPHTKEPRLFSICKHVLVKDIKIIVLDLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.1846
R free: 0.2137
Average B factor: 37.279
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG 1500, 0.2M NaCl, 0.1M HEPES pH7.5
Matthews coefficient: 2.19
Solvent content (%): 43.78
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: 2021-08-25
RPA70N-MRE11 fusion (PDB entry 8K00)
Macromolecule: Replication protein A 70 kDa DNA-binding subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 121 residues
Sequence: SMVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1731
R free: 0.1988
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Ammonium sulate
Matthews coefficient: 1.77
Solvent content (%): 30.69
Release date: 2023-09-13
Human DNA polymerase beta crosslinked complex, 60 s Ca to Mn exchange (PDB entry 7RBM)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 341 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.2045
R free: 0.247
Average B factor: 42.531
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Citrate pH 5.5, 18% PEG6000
Matthews coefficient: 2.13
Solvent content (%): 42.33
Ligand: 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol (QPJ)
Ligand formula: C5 H14 O10 P2
Ligand molecular weight: 296.106
Ligand SMILES: C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1
Release date: 2022-03-09
Crystal Structure of CK2alpha with Compound 1 bound (PDB entry 6YPJ)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.195
R free: 0.2323
Average B factor: 32.33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.04
Solvent content (%): 39.59
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2020-07-15