satarupa22/MacromolecularLigandDB huggingface dataset:
Cathepsin-K in complex with MIV-711 (PDB entry 6QL8)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 217 residues
Sequence: GRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.149
R free: 0.1811
Average B factor: 17.394
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 100mM ADA pH6.0, 500mM ammonium nitrate, 17% PEG 3350
Matthews coefficient: 2.87
Solvent content (%): 57.2
Ligand: ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-ethynyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide (J5N)
Ligand formula: C29 H36 F N5 O4 S
Ligand molecular weight: 569.691
Ligand SMILES: CC(C)CC(C(=O)N1CC(C2C1C(CO2)O)C#C)NC(=O)c3ccc(cc3)c4c(sc(n4)N5CCN(CC5)C)F
Ligand InChI: InChI=1S/C29H36FN5O4S/c1-5-18-15-35(24-22(36)16-39-25(18)24)28(38)21(14-17(2)3)31-27(37)20-8-6-19(7-9-20)23-26(30)40-29(32-23)34-12-10-33(4)11-13-34/h1,6-9,17-18,21-22,24-25,36H,10-16H2,2-4H3,(H,31,37)/t18-,21+,22+,24-,25-/m1/s1
Release date: 2020-02-19
PTPN21 PTP domain C1108S mutant in complex with SRC pTyr530 peptide (PDB entry 8GWH)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 21
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 299 residues
Sequence: TRATNDERCKILEQRLEQGMVFTEYERILKKRLVDGECSTARLPENAERNRFQDVLPYDDVRVELVPTKENNTGYINASHIKVSVSGIEWDYIATQGPLQNTCQDFWQMVWEQGIAIIAMVTAEEEGGREKSFRYWPRLGSRHNTVTYGRFKITTRFRTDSGCYATTGLKMKHLLTGQERTVWHLQYTDWPEHGCPEDLKGFLSYLEEIQSVRRHTNSTSDPQSPNPPLLVHSSAGVGRTGVVILSEIMIACLEHNEVLDIPRVLDMLRQQRMMLVQTLCQYTFVYRVLIQFLKSSRLI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.181
R free: 0.2097
Average B factor: 46.8635
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 278
Crystal growth procedure: sodium acetate, PEG 4000
Matthews coefficient: 2.8
Solvent content (%): 56.14
Release date: 2023-09-20
Mek1 adopts DFG-out conformation when bound to an analog of E6201. (PDB entry 5HZE)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 348 residues
Sequence: GLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLNKFGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.20053
R free: 0.28714
Average B factor: 69.241
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris pH 8.0, 180 mM CaCl2, 14-18% PEG 4000. Co-crystallized with 1mM ATPgammaS (30 mM stock formulated in H2O). Crystals backsoaked for 2 weeks in 1 mM compound 3.3% DMSO final.
Matthews coefficient: 2.45
Solvent content (%): 49.75
Ligand: (3S,4R,8S,9S,11E)-8,9,16-trihydroxy-3,4-dimethyl-14-(methylamino)-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione (E62)
Ligand formula: C20 H27 N O6
Ligand molecular weight: 377.431
Ligand SMILES: CC1CCC(=O)C(C(CC=Cc2cc(cc(c2C(=O)OC1C)O)NC)O)O
Ligand InChI: InChI=1S/C20H27NO6/c1-11-7-8-16(23)19(25)15(22)6-4-5-13-9-14(21-3)10-17(24)18(13)20(26)27-12(11)2/h4-5,9-12,15,19,21-22,24-25H,6-8H2,1-3H3/b5-4+/t11-,12+,15+,19+/m1/s1
Release date: 2017-05-03
Crystal structure of human GPX4-U46C-R152H in complex with TMT10 (PDB entry 7U4J)
Macromolecule: Phospholipid hydroperoxide glutathione peroxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.1.12
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEAASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKHYGPMEEPLVIEKDLPHYF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.1703
R free: 0.2051
Average B factor: 25.2478
Crystallization method: MICROBATCH
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M potassium thiocyanate and 20% (w/v) PEG 3350
Matthews coefficient: 2.21
Solvent content (%): 44.47
Ligand: ~{N}-(3-chloranyl-4-methoxy-phenyl)ethanamide (8NB)
Ligand formula: C9 H10 Cl N O2
Ligand molecular weight: 199.634
Ligand SMILES: CC(=O)Nc1ccc(c(c1)Cl)OC
Ligand InChI: InChI=1S/C9H10ClNO2/c1-6(12)11-7-3-4-9(13-2)8(10)5-7/h3-5H,1-2H3,(H,11,12)
Release date: 2022-12-07
Crystal Structure of human phosphodiesterase 10 in complex with 4-N-(2-fluoroethyl)-4-N,2-dimethyl-3-N-(2-phenyl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)pyrazole-3,4-dicarboxamide (PDB entry 5SER)
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): 2.25
R work: 0.1724
R free: 0.2329
Average B factor: 49.942
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: 2.62
Solvent content (%): 53.01
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
caspase-1 P20/P10 C285A in complex with human GSDMD-C domain (PDB entry 6KN0)
Macromolecule: Caspase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.36
Sequence length: 167 residues
Sequence: GNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQAARGDSPGVVWFKD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.793
R work: 0.2403
R free: 0.2997
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000
Matthews coefficient: 2.29
Solvent content (%): 46.19
Release date: 2020-03-11
Crystal structure of DYRK1B in complex with AZ191 (PDB entry 8C2Z)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 372 residues
Sequence: MDSSNKKEKKVLNHGYDDDNHDYIVRSGERWLERYEIDSLIGKGSFGQVVKAYDHQTQELVAIKIIKNKKAFLNQAQIELRLLELMNQHDTEMKYYIVHLKRHFMFRNHLCLVFELLSYNLYDLLRNTHFRGVSLNLTRKLAQQLCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGTPYDLAIDMWSLGCILVEMHTGEPLFSGSNEVDQMNRIVEVLGIPPAAMLDQAPKARKYFERLPGGGWTLRRTKELRKDYQGPGTRRLQEVLGVQTGGPGGRRAGEPGHSPADYLRFQDLVLRMLEYEPAARISPLGALQHGFFRRTADEATNTGENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.1767
R free: 0.2196
Average B factor: 49.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 25% PEG3350, 0.2 M magnesium chloride, 0.1 M manganese (II) chloride.
Matthews coefficient: 2.22
Solvent content (%): 44.5
Ligand: N-[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]-4-(1-methylpyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine (QS0)
Ligand formula: C24 H27 N7 O
Ligand molecular weight: 429.517
Ligand SMILES: Cn1cc(c2c1cncc2)c3ccnc(n3)Nc4ccc(cc4OC)N5CCN(CC5)C
Ligand InChI: InChI=1S/C24H27N7O/c1-29-10-12-31(13-11-29)17-4-5-21(23(14-17)32-3)28-24-26-9-7-20(27-24)19-16-30(2)22-15-25-8-6-18(19)22/h4-9,14-16H,10-13H2,1-3H3,(H,26,27,28)
Release date: 2024-01-17
Crystal Structure of CK2alpha with N-((2-chloro-[1,1'-biphenyl]-4-yl)methyl)butane-1,4-diamine bound (PDB entry 5MMR)
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): 2
R work: 0.1958
R free: 0.2257
Average B factor: 38.24
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: 2.2
Solvent content (%): 44.07
Ligand: ~{N}'-[(3-chloranyl-4-phenyl-phenyl)methyl]butane-1,4-diamine (H83)
Ligand formula: C17 H21 Cl N2
Ligand molecular weight: 288.815
Ligand SMILES: c1ccc(cc1)c2ccc(cc2Cl)CNCCCCN
Ligand InChI: InChI=1S/C17H21ClN2/c18-17-12-14(13-20-11-5-4-10-19)8-9-16(17)15-6-2-1-3-7-15/h1-3,6-9,12,20H,4-5,10-11,13,19H2
Release date: 2017-05-24
Crystal structure of human CLK1 in complex with compound 25 (PDB entry 5X8I)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 346 residues
Sequence: MHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSILEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.902
R work: 0.1661
R free: 0.2064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 291
Crystal growth procedure: 2% (v/v) PEG 200, 20% (v/v) tacsimate (pH 7.0), 0.1M HEPES (pH 9.0)
Matthews coefficient: 2.37
Solvent content (%): 48.17
Ligand: 5-[1-[(1S)-1-(4-fluorophenyl)ethyl]-[1,2,3]triazolo[4,5-c]quinolin-8-yl]-1,3-benzoxazole (SQZ)
Ligand formula: C24 H16 F N5 O
Ligand molecular weight: 409.415
Ligand SMILES: CC(c1ccc(cc1)F)n2c3c4cc(ccc4ncc3nn2)c5ccc6c(c5)nco6
Ligand InChI: InChI=1S/C24H16FN5O/c1-14(15-2-6-18(25)7-3-15)30-24-19-10-16(4-8-20(19)26-12-22(24)28-29-30)17-5-9-23-21(11-17)27-13-31-23/h2-14H,1H3/t14-/m0/s1
Release date: 2017-08-16
Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion (PDB entry 8V7B)
Macromolecule: DNA (5'-D(*CP*AP*TP*GP*AP*TP*GP*AP*CP*GP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 12 residues
Sequence: CATGATGACGCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1765
R free: 0.2146
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.12
Solvent content (%): 41.85
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: 2024-05-15
Complex structure of human protein kinase CK2 catalytic subunit with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) crystallized under low-salt conditions (PDB entry 5M4F)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.519
R work: 0.1628
R free: 0.1826
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PROTEIN STOCK SOLUTION: 6 MG/ML CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; 

INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO;

PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; 

RESERVOIR SOLUTION: 24 % PEG3350, 0.2 M KCl; 

DROP SOLUTION BEFORE EQULIBRATION: 0.5 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.5 MICROLITER RESERVOIR SOLUTION
Matthews coefficient: 1.96
Solvent content (%): 37.21
Ligand: 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid (7FC)
Ligand formula: C16 H8 Cl2 O5
Ligand molecular weight: 351.138
Ligand SMILES: c1cc(ccc1C2=C(C(=O)c3cc(cc(c3O2)Cl)Cl)O)C(=O)O
Ligand InChI: InChI=1S/C16H8Cl2O5/c17-9-5-10-12(19)13(20)14(23-15(10)11(18)6-9)7-1-3-8(4-2-7)16(21)22/h1-6,20H,(H,21,22)
Release date: 2017-01-18
Crystal Structure of BACE1 in complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo-2,9lambda6-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide (PDB entry 6JSN)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 416 residues
Sequence: GSHMLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2006
R free: 0.2585
Average B factor: 44.745
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2 M sodium citrate, 0.2 M ammonium iodide, 19%(w/v) polyethylene glycol 5000 monomethyl ether, pH 6.5
Matthews coefficient: 3
Solvent content (%): 59.06
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2019-08-28
Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable dTTP WITH MANGANESE IN THE ACTIVE SITE (PDB entry 4YN4)
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): 2.243
R work: 0.2026
R free: 0.2547
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.39
Solvent content (%): 48.49
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: 2016-03-09
Human cytosolic 5' nucleotidase IIIB (PDB entry 7ZEE)
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): 1.36
R work: 0.1586
R free: 0.1965
Average B factor: 28.56
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.2
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M MES pH 6.2, 27% PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.77
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2022-04-13
Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II (PDB entry 5EGB)
Macromolecule: DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 21 residues
Sequence: ACCACGTGGCTAGGGAGGCCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.977
R work: 0.1925
R free: 0.2196
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.055M Bis-Tris propane, 0.045M Citric Acid, 30% PEG3350
Matthews coefficient: 3.12
Solvent content (%): 60.61
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: 2016-02-17
Crystal structure of human METTL1 in complex with SAM (PDB entry 8D59)
Macromolecule: tRNA (guanine-N(7)-)-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.33
Sequence length: 262 residues
Sequence: MHHHHHHENLYFQGSGYYRQRAHSNPMADHTLRYPVKPEEMDWSELYPEFFAPLTQNQSHDDPKDKKEKRAQAQVEFADIGCGYGGLLVELSPLFPDTLILGLEIRVKVSDYVQDRIRALRAAPAGGFQNIACLRSNAMKHLPNFFYKGQLTKMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGLVYTITDVLELHDWMCTHFEEHPLFERVPLEDLSEDPVVGHLGTSTEEGKKVLRNGGKNFPAIFRRIQDPVLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.2073
R free: 0.2295
Average B factor: 53.48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 295.15
Crystal growth procedure: 50 mM Sodium cacodylate pH 5.7, 1.5 M Lithium sulfate, 10 mM Magnesium sulfate
Matthews coefficient: 2.46
Solvent content (%): 50.03
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2023-01-11
Crystal structure of human lysosomal acid-alpha-glucosidase, GAA (PDB entry 5NN3)
Macromolecule: Lysosomal alpha-glucosidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.20
Sequence length: 872 residues
Sequence: QCDVPPNSRFDCAPDKAITQEQCEARGCCYIPAKQGLQGAQMGQPWCFFPPSYPSYKLENLSSSEMGYTATLTRTTPTFFPKDILTLRLDVMMETENRLHFTIKDPANRRYEVPLETPRVHSRAPSPLYSVEFSEEPFGVIVHRQLDGRVLLNTTVAPLFFADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGANLYGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSSTAITRQVVENMTRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPAISSSGPAGSYRPYDEGLRRGVFITNETGQPLIGKVWPGSTAFPDFTNPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVPGVVGGTLQAATICASSHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGADVCGFLGNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTVDHQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPIEALGSLPPPPAAPREPAIHSEGQWVTLPAPLDTINVHLRAGYIIPLQGPGLTTTESRQQPMALAVALTKGGEARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVLGVATAPQQVLSNGVPVSNFTYSPDTKVLDICVSLLMGEQFLVSWC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.16195
R free: 0.18874
Average B factor: 33.138
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.9 M ammonium sulfate, 0.1 M HEPES pH 7.0, 2% v/v PEG400
Matthews coefficient: 3.32
Solvent content (%): 62.94
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: 2017-10-25
CDK2 in complex with FragLite36 (PDB entry 6Q4H)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.0
R work: 0.19098
R free: 0.20663
Average B factor: 18.136
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Matthews coefficient: 1.99
Solvent content (%): 38.06
Ligand: 2-[3-[(2-azanyl-9~{H}-purin-6-yl)oxy]phenyl]ethanoic acid (HGH)
Ligand formula: C13 H11 N5 O3
Ligand molecular weight: 285.258
Ligand SMILES: c1cc(cc(c1)Oc2c3c([nH]cn3)nc(n2)N)CC(=O)O
Ligand InChI: InChI=1S/C13H11N5O3/c14-13-17-11-10(15-6-16-11)12(18-13)21-8-3-1-2-7(4-8)5-9(19)20/h1-4,6H,5H2,(H,19,20)(H3,14,15,16,17,18)
Release date: 2019-03-20