satarupa22/MacromolecularLigandDB huggingface dataset:
Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mM Mn2+ for 1800s then with 10 mM Mn2+ for 60s (PDB entry 5KG3)
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: 0.1972
R free: 0.2366
Average B factor: 22.7138
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 (%): 40.9
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
Binary complex of DNA Polymerase Beta with Fapy-dG in the template position (PDB entry 7S9N)
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): 1.71
R work: 0.1916
R free: 0.2364
Average B factor: 27.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
Matthews coefficient: 2.35
Solvent content (%): 47.65
Release date: 2022-08-03
Crystal Structure of human phosphodiesterase 10 in complex with 6-chloro-2,3-dimethylquinoxaline (PDB entry 5SJQ)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.185
R free: 0.223
Average B factor: 44.155
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.63
Solvent content (%): 53.18
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-10-12
Two intermediate states of conformation switch in dual specificity phosphatase 13a (PDB entry 5XJV)
Macromolecule: Dual specificity protein phosphatase 13 isoform A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 185 residues
Sequence: MAETSLPELGGEDKATPAPSILELEELLRAGKSSASRVDEVWPNLFIGDAATANNRFELWKLGITHVLNAAHKGLYAQGGPDFYGSSVSYLGVPAHDLPDFDISAYFSSAADFIHRALNTPGAKVLVHSVVGVSRSATLVLAYLMLHQRLSLRQAVITVRQHRWVFPNRGFLHQLARLDQQLRGA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.17786
R free: 0.22057
Average B factor: 20.38
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Tris-HCl (pH 8.5), 20% ethanol
Matthews coefficient: 2.03
Solvent content (%): 39.27
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2018-04-11
Human PIM1 bound to benzothiophene inhibitor 354 (PDB entry 6PDO)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: SMLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1753
R free: 0.223
Average B factor: 66.072
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 0.1 M HEPES pH7.5, 0.2 M magnesium chloride
Matthews coefficient: 2.86
Solvent content (%): 56.98
Ligand: 4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxamide (OD1)
Ligand formula: C17 H17 N3 O2 S2
Ligand molecular weight: 359.466
Ligand SMILES: c1cc(c2cc(sc2c1)C(=O)N)c3ccc(s3)C(=O)NCCCN
Ligand InChI: InChI=1S/C17H17N3O2S2/c18-7-2-8-20-17(22)14-6-5-13(23-14)10-3-1-4-12-11(10)9-15(24-12)16(19)21/h1,3-6,9H,2,7-8,18H2,(H2,19,21)(H,20,22)
Release date: 2019-07-24
A fragment-based inhibitor of SHP2 (PDB entry 8S0S)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 537 residues
Sequence: HMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.21494
R free: 0.25846
Average B factor: 47.359
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M K formate
15% PEG 3350
0.1M pH=8 Bis-Tris propane/HCl
Matthews coefficient: 2.19
Solvent content (%): 43.78
Ligand: (1R,5S)-8-[7-(4-chloranyl-2-methyl-indazol-5-yl)-5H-pyrrolo[2,3-b]pyrazin-3-yl]-8-azabicyclo[3.2.1]octan-3-amine (A1H4H)
Ligand formula: C21 H22 Cl N7
Ligand molecular weight: 407.899
Ligand SMILES: Cn1cc2c(n1)ccc(c2Cl)c3c[nH]c4c3ncc(n4)N5C6CCC5CC(C6)N
Ligand InChI: InChI=1S/C21H22ClN7/c1-28-10-16-17(27-28)5-4-14(19(16)22)15-8-25-21-20(15)24-9-18(26-21)29-12-2-3-13(29)7-11(23)6-12/h4-5,8-13H,2-3,6-7,23H2,1H3,(H,25,26)/t11-,12+,13-
Release date: 2024-03-20
TRIM7 in complex with C-terminal peptide of 2C (PDB entry 7W0T)
Macromolecule: E3 ubiquitin-protein ligase TRIM7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 174 residues
Sequence: KEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1683
R free: 0.1864
Average B factor: 21.77
Crystallization method: LIQUID DIFFUSION
Crystallization temperature (K): 291.15
Crystal growth procedure: ammonium acetate, magnesium acetate tetrahydrate, HEPES sodium, polyethylene glycol
Matthews coefficient: 2.43
Solvent content (%): 49.48
Release date: 2022-08-10
Crystal structure of KRAS G12D with compound 36 (4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-7-(8-ethynyl-7-fluoronaphthalen-1-yl)-8-fluoro-2-{[(4s,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidine) bound (PDB entry 7RT5)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1625
R free: 0.1872
Average B factor: 20.0976
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium citrate, pH 4.5, 26% PEG8000, 200 mM ammonium acetate
Matthews coefficient: 2.37
Solvent content (%): 48.1
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: 2021-12-22
Protein Tyrosine Phosphatase 1B P185G mutant, open state (PDB entry 5KAC)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 306 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVGESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1681
R free: 0.2109
Average B factor: 31.7259
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris, pH 7.4, 0.2 M MgCl2, 18% PEG8000
Matthews coefficient: 2.51
Solvent content (%): 51.04
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: 2017-03-08
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Imidazo-pyridine 24 (PDB entry 6MDD)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.213
R free: 0.251
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG3350, 200MM AMMONIUM PHOSPHATE
Matthews coefficient: 2.3
Solvent content (%): 46.53
Ligand: 5-[(2,3-dichlorophenyl)sulfanyl]-3H-imidazo[4,5-b]pyridin-2-amine (JE7)
Ligand formula: C12 H8 Cl2 N4 S
Ligand molecular weight: 311.19
Ligand SMILES: c1cc(c(c(c1)Cl)Cl)Sc2ccc3c(n2)[nH]c(n3)N
Ligand InChI: InChI=1S/C12H8Cl2N4S/c13-6-2-1-3-8(10(6)14)19-9-5-4-7-11(17-9)18-12(15)16-7/h1-5H,(H3,15,16,17,18)
Release date: 2019-02-13
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5ORY)
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): 1.99
R work: 0.2043
R free: 0.2654
Average B factor: 61.3357
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: 2.79
Solvent content (%): 55.86
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2017-11-01
WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) (PDB entry 5HQG)
Macromolecule: E3 ubiquitin-protein ligase RFWD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 362 residues
Sequence: HHHHHHMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAANSQGTIKVLELV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2105
R free: 0.2417
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium nitrate 0.5M
10% PEG 3350
Matthews coefficient: 2.24
Solvent content (%): 45.13
Release date: 2016-04-20
Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing spiroiminodihydantoin (Sp) (PDB entry 6LWD)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MGQGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.2111
R free: 0.254
Average B factor: 72.969
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.75
Solvent content (%): 55.29
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: 2021-06-09
DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 60 min (PDB entry 7M47)
Macromolecule: DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 7 residues
Sequence: CAGTACT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.648
R work: 0.1797
R free: 0.2082
Average B factor: 39.3116
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.82
Solvent content (%): 56.45
Ligand: S,R MESO-TARTARIC ACID (SRT)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2+
Release date: 2022-07-06
Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink (PDB entry 6U2O)
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): 2.3
R work: 0.201
R free: 0.2481
Average B factor: 38.251
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295.15
Crystal growth procedure: 23% PEG 3350, 50 mM Tris (pH 6.5), and 350 mM sodium acetate
Matthews coefficient: 2.37
Solvent content (%): 48.02
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: 2020-08-26
Crystal structure of TNKS2 in complex with 2-(4-chlorophenyl)-1,2,3,4- tetrahydroquinazolin-4-one (PDB entry 5AKW)
Macromolecule: TANKYRASE-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.17603
R free: 0.2115
Average B factor: 29.431
Crystallization pH: 8.5
Crystal growth procedure: pH 8.5
Matthews coefficient: 2.4
Solvent content (%): 49
Ligand: (2S)-2-(4-chlorophenyl)-2,3-dihydro-1H-quinazolin-4-one (NKI)
Ligand formula: C14 H11 Cl N2 O
Ligand molecular weight: 258.703
Ligand SMILES: c1ccc2c(c1)C(=O)NC(N2)c3ccc(cc3)Cl
Ligand InChI: InChI=1S/C14H11ClN2O/c15-10-7-5-9(6-8-10)13-16-12-4-2-1-3-11(12)14(18)17-13/h1-8,13,16H,(H,17,18)/t13-/m0/s1
Release date: 2015-07-29
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate/ADP/Mn after reaction (PDB entry 8PPJ)
Macromolecule: Inositol-trisphosphate 3-kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.127
Sequence length: 279 residues
Sequence: GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.19706
R free: 0.23423
Average B factor: 40.128
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.80 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. 
Protein:precipitant ratio 1:1. 
Protein concentration: 17 mg/ml. 
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. 
Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.
Matthews coefficient: 2.68
Solvent content (%): 54.1
Ligand: beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate (661)
Ligand formula: C7 H18 O18 P4
Ligand molecular weight: 514.102
Ligand SMILES: C(C1C(C(C(C(O1)COP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C7H18O18P4/c8-5-3(1-21-26(9,10)11)23-4(2-22-27(12,13)14)6(24-28(15,16)17)7(5)25-29(18,19)20/h3-8H,1-2H2,(H2,9,10,11)(H2,12,13,14)(H2,15,16,17)(H2,18,19,20)/t3-,4+,5-,6+,7+/m0/s1
Release date: 2024-02-28
BMP1 complexed with a reverse hydroxamate - compound 4 (PDB entry 6BSM)
Macromolecule: Bone morphogenetic protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.19
Sequence length: 201 residues
Sequence: XAATSRPERVWPDGVIPFVIGGNFTGSQRAVFRQAMRHWEKHTCVTFLERTDEDSYIVFTYRPCGCCSYVGRRGGGPQAISIGKNCDKFGIVVHELGHVVGFWHEHTRPDRDRHVSIVRENIQPGQEYNFLKMEPQEVESLGETYDFDSIMHYARNTFSRGIFLDTIVPKYEVNGVKPPIGQRTRLSKGDIAQARKLYKCP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.1923
R free: 0.2245
Average B factor: 57.112
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 5% PEG3350, 200 mM KSCN, 10mM spermadine
Matthews coefficient: 3.83
Solvent content (%): 67.92
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2018-08-08
Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA (PDB entry 7MZ3)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.418
R work: 0.2039
R free: 0.2662
Average B factor: 36.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.42
Solvent content (%): 49.27
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-06-01