satarupa22/MacromolecularLigandDB huggingface dataset:
PTPN21 FERM (PDB entry 8GVL)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 21
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 301 residues
Sequence: SSKSCLVARIQLLNNEFVEFTLSVESTGQESLEAVAQRLELREVTYFSLWYYNKQNQRRWVDLEKPLKKQLDKYALEPTVYFGVVFYVPSVSQLQQEITRYQYYLQLKKDILEGSIPCTLEQAIQLAGLAVQADFGDFDQYESQDFLQKFALFPVGWLQDEKVLEEATQKVALLHQKYRGLTAPDAEMLYMQEVERMDGYGEESYPAKDSQGSDISIGACLEGIFVKHKNGRHPVVFRWHDIANMSHNKSFFALELANKEETIQFQTEDMETAKYIWRLCVARHKFYRLNQCNLQTQTVTV
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1925
R free: 0.2296
Average B factor: 50.1404
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: MPD
Matthews coefficient: 2.64
Solvent content (%): 53.43
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2023-09-20
Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine (PDB entry 5ULW)
Macromolecule: DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3')
Type: DNA, polydeoxyribonucleotide
Source organism: unidentified
Sequence length: 7 residues
Sequence: AGGACCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.617
R work: 0.2038
R free: 0.2484
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 50 mM MES, pH 6.0, 18 % PEG 5KMME, 0.4 M Ammonium Sulfate
Matthews coefficient: 2.67
Solvent content (%): 53.93
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2017-04-19
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 3,5-(PCP)2-IP4 (PDB entry 5DGI)
Macromolecule: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.21
Sequence length: 330 residues
Sequence: GSFTERQIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENWPLCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSILQAEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSAEDHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMPTDGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREKLIAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKILGNIVMRELAPQFHIPWSIPLEAED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.15005
R free: 0.20252
Average B factor: 28.079
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight,while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM compound.
Matthews coefficient: 2.67
Solvent content (%): 53.92
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: 2016-08-10
Crystal Structure of human phosphodiesterase 10 in complex with 5-methyl-2-phenyl-4-(2-quinolin-8-yloxyethyl)-1,3-oxazole (PDB entry 5SH1)
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): 2.2
R work: 0.1862
R free: 0.2313
Average B factor: 36.905
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: 2.64
Solvent content (%): 53.45
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: 2022-10-12
SUBSTITUTED BENZYLOXYTRICYCLIC COMPOUNDS AS RETINOIC ACID-RELATED ORPHAN RECEPTOR GAMMA T AGONISTS (PDB entry 6W9I)
Macromolecule: Nuclear receptor ROR-gamma, Steroid receptor coactivator 1 fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 285 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFSTSGGSGGLTERHKILHRLLQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.608
R work: 0.1933
R free: 0.2355
Average B factor: 27.62
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: protein at 8-10mg/ml, with 0.2M MgCl2, 22% PEG3350, 0.1M Bis-Tris pH 5.5
Matthews coefficient: 2.29
Solvent content (%): 46.21
Ligand: 1-(benzyloxy)-4-{1-[(4-fluorophenyl)sulfonyl]cyclopentyl}benzene (Z7D)
Ligand formula: C24 H23 F O3 S
Ligand molecular weight: 410.501
Ligand SMILES: c1ccc(cc1)COc2ccc(cc2)C3(CCCC3)S(=O)(=O)c4ccc(cc4)F
Ligand InChI: InChI=1S/C24H23FO3S/c25-21-10-14-23(15-11-21)29(26,27)24(16-4-5-17-24)20-8-12-22(13-9-20)28-18-19-6-2-1-3-7-19/h1-3,6-15H,4-5,16-18H2
Release date: 2020-04-29
A SETD3 Mutant (N255A) in Complex with an Actin Peptide with His73 Replaced with Lysine (PDB entry 6OX5)
Macromolecule: Actin Peptide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 18 residues
Sequence: TLKYPIEKGIVTNWDDME
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.098
R work: 0.1627
R free: 0.2048
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000
Matthews coefficient: 2.2
Solvent content (%): 44.09
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2019-08-21
Peptide LLKVAL in complex with human cathepsin V C25S mutant (PDB entry 7Q8P)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 222 residues
Sequence: DLPKSVDWRKKGYVTPVKNQKQCGSSWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1764
R free: 0.1991
Average B factor: 30.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 77 % MPD, 23 % of 60 mM TRIS, pH 8
Matthews coefficient: 2.84
Solvent content (%): 56.72
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: 2022-11-23
Crystal structure of methyladenine demethylase (PDB entry 6IE3)
Macromolecule: Nucleic acid dioxygenase ALKBH1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.51
Sequence length: 389 residues
Sequence: MGKMAAAVGSVATLATEPGEDAFRKLFRFYRQSRPGTADLEGVIDFSAAHAARGKGPGAQKVIKSQLNVSSVSEQNAYRAGLQPVSKWQAYGLKGYPGFIFIPNPFLPGYQWHWVKQCLKLYSQKPNVCNLDKHMSKEETQDLWEQSKEFLRYKEATKRRPRSLLEKLRWVTVGYHYNWDSKKYSADHYTPFPSDLGFLSEQVAAACGFEDFRAEAGILNYYRLDSTLGIHVDRSELDHSKPLLSFSFGQSAIFLLGGLQRDEAPTAMFMHSGDIMIMSGFSRLLNHAVPRVLPNPEGEGLPHCLEAPLPAVLPRDSMVEPCSMEDWQVCASYLKTARVNMTVRQVLATDQNFPLEPIEDEKRDISTEGFCHLDDQNSEVKRARINPDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.20253
R free: 0.2331
Average B factor: 31.318
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 286
Crystal growth procedure: 5% ethanol, 5% MPD, 100 mM NaF, 100 mM HepespH7.5
Matthews coefficient: 2.03
Solvent content (%): 39.35
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: 2019-09-18
Crystal structure of SARS-CoV papain-like protease in complex with the C-terminal domain of human ISG15 (PDB entry 5TL6)
Macromolecule: Replicase polyprotein 1ab
Type: Protein, polypeptide(L)
Source organism: Severe acute respiratory syndrome-related coronavirus
EC number: 3.4.19.12
Sequence length: 319 residues
Sequence: MASMEVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.618
R work: 0.1909
R free: 0.2496
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M lithium sulfate, 0.1 M Bis-tris [pH 6.5], 22% PEG 3350, supplemented with 30% (v/v) glycerol additive in a 1:5 dilution
Matthews coefficient: 2.53
Solvent content (%): 51.34
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: 2017-05-03
Crystal structure of human polymerase eta complexed with syn N7-acetophenoneguanine (PDB entry 7LCD)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1823
R free: 0.2091
Average B factor: 33.57
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES pH 6.5 
20% PEG2000 MME 
5 mM magnesium chloride
Matthews coefficient: 2.11
Solvent content (%): 41.82
Release date: 2022-02-09
The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH7.4 (PDB entry 5YC7)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 246 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.21192
R free: 0.26158
Average B factor: 55.99
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate (pH 4.6), 2.0M ammonium sulfate supplemented with 5% PEG 400
Matthews coefficient: 2.17
Solvent content (%): 43.22
Ligand: 1-(4-BROMOPHENYL)METHANAMINE (PZH)
Ligand formula: C7 H8 Br N
Ligand molecular weight: 186.049
Ligand SMILES: c1cc(ccc1CN)Br
Ligand InChI: InChI=1S/C7H8BrN/c8-7-3-1-6(5-9)2-4-7/h1-4H,5,9H2
Release date: 2018-10-03
Crystal structure of WT KRAS4a with bound GMPPNP and Mg ion (PDB entry 8T72)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 178 residues
Sequence: GMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1917
R free: 0.2362
Average B factor: 50.3754
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M NaBr, 20% PEG 3350
Matthews coefficient: 1.81
Solvent content (%): 31.96
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2024-02-14
PanDDA analysis group deposition of ground-state model of PTP1B (PDB entry 7FRS)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.16
R free: 0.1901
Average B factor: 40.734
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.3
Solvent content (%): 62.7
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2022-11-23
Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker (PDB entry 8UQ8)
Macromolecule: E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 437 residues
Sequence: GHMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGSGSGSGSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAMGSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.34
R work: 0.1959
R free: 0.2357
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 288
Crystal growth procedure: Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Matthews coefficient: 3.89
Solvent content (%): 68.41
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: 2024-01-17
Specific covalent inhibitor(10) of ERK2 (PDB entry 8AO9)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.624
R work: 0.1811
R free: 0.2324
Average B factor: 26.199
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.3
Solvent content (%): 46.54
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2022-09-28
The ligand-free structure of human PPARgamma LBD F287Y mutant in the presence of the SRC-1 coactivator peptide (PDB entry 7CXI)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 283 residues
Sequence: AEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQYRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2434
R free: 0.2761
Average B factor: 41.091
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 295
Crystal growth procedure: 2.2 M sodium malonate (pH 7.0)
Matthews coefficient: 2.71
Solvent content (%): 54.59
Ligand: MALONATE ION (MLI)
Ligand formula: C3 H2 O4
Ligand molecular weight: 102.046
Ligand SMILES: C(C(=O)[O-])C(=O)[O-]
Ligand InChI: InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2
Release date: 2021-09-01
The crystal structure of nickel bound human ADO C18S C239S variant (PDB entry 7REI)
Macromolecule: 2-aminoethanethiol dioxygenase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.19
Sequence length: 270 residues
Sequence: MPRDNMASLIQRIARQASLTFRGSGGGRGASDRDAASGPEAPMQPGFPENLSKLKSLLTQLRAEDLNIAPRKATLQPLPPNLPPVTYMHIYETDGFSLGVFLLKSGTSIPLHDHPGMHGMLKVLYGTVRISCMDKLDAGGGQRPRALPPEQQFEPPLQPREREAVRPGVLRSRAEYTEASGPCILTPHRDNLHQIDAVEGPAAFLDILAPPYDPDDGRDCHYYRVLEPVRPKEASSSASDLPREVWLLETPQADDFWCEGEPYPGPKVFP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1801
R free: 0.2093
Average B factor: 32.4678
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M LiSO4, 0.1 M Bis-Tris pH 5.5, 20% w/v PEG 3350
Matthews coefficient: 2.6
Solvent content (%): 52.63
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2021-09-15
IRAK4 in complex with compound 24 (PDB entry 8TVM)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 307 residues
Sequence: ENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2212
R free: 0.2465
Average B factor: 62.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Sodium Malonate
Matthews coefficient: 2.6
Solvent content (%): 52.69
Ligand: N-{1-[(1R,2R)-2-fluorocyclopropyl]-2-oxo-1,2-dihydropyridin-3-yl}-2-[(1R,4r)-1-methyl-2-oxabicyclo[2.1.1]hexan-4-yl]-6-[(propan-2-yl)oxy]-2H-pyrazolo[3,4-b]pyridine-5-carboxamide (VDC)
Ligand formula: C24 H26 F N5 O4
Ligand molecular weight: 467.493
Ligand SMILES: CC(C)Oc1c(cc2cn(nc2n1)C34CC(C3)(OC4)C)C(=O)NC5=CC=CN(C5=O)C6CC6F
Ligand InChI: InChI=1S/C24H26FN5O4/c1-13(2)34-21-15(20(31)26-17-5-4-6-29(22(17)32)18-8-16(18)25)7-14-9-30(28-19(14)27-21)24-10-23(3,11-24)33-12-24/h4-7,9,13,16,18H,8,10-12H2,1-3H3,(H,26,31)/t16-,18+,23-,24-/m0/s1
Release date: 2024-06-26
Crystal structure of CREBBP bromodomain complexed with FA26 (PDB entry 5MPN)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.23
R work: 0.1582
R free: 0.1674
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M MgCl2, 0.1 M Bis-Tris, pH6.5, 5% EG, 23% PEG3350
Matthews coefficient: 2.13
Solvent content (%): 42.24
Ligand: 1-[4-ethoxy-3-[3-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]ethanone (YE5)
Ligand formula: C17 H16 N4 O2
Ligand molecular weight: 308.335
Ligand SMILES: CCOc1ccc(cc1c2cccc(c2)c3n[nH]nn3)C(=O)C
Ligand InChI: InChI=1S/C17H16N4O2/c1-3-23-16-8-7-12(11(2)22)10-15(16)13-5-4-6-14(9-13)17-18-20-21-19-17/h4-10H,3H2,1-2H3,(H,18,19,20,21)
Release date: 2018-01-17