satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide (PDB entry 8YTE)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 102 residues
Sequence: NVSFPASVQLHTAVEMHHWCIPFSVDGQPAPSLRWLFNGSVLNETSFIFTEFLEPAANETVRHGCLRLNQPTHVNNGNYTLLAANPFGQASASIMAAFMDNP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.19668
R free: 0.24947
Average B factor: 29.8
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate
Matthews coefficient: 2.69
Solvent content (%): 54.3
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: 2024-07-10
Structure of the Human mitochondrial kinase COQ8A R611K with AMPPNP (Cerebellar Ataxia and Ubiquinone Deficiency Through Loss of Unorthodox Kinase Activity) (PDB entry 5I35)
Macromolecule: Atypical kinase ADCK3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7
Sequence length: 393 residues
Sequence: SSEANAERIVRTLCKVRGAALKLGQMLSIQDDAFINPHLAKIFERVRQSADFMPLKQMMKTLNNDLGPNWRDKLEYFEERPFAAASIGQVHLARMKGGREVAMKIQYPGVAQSINSDVNNLMAVLNMSNMLPEGLFPEHLIDVLRRELALECDYQREAACARKFRDLLKGHPFFYVPEIVDELCSPHVLTTELVSGFPLDQAEGLSQEIRNEICYNILVLCLRELFEFHFMQTDPNWSNFFYDPQQHKVALLDFGATREYDRSFTDLYIQIIRAAADRDRETVRAKSIEMKFLTGYEVKVMEDAHLDAILILGEAFASDEPFDFGTQSTTEKIHNLIPVMLRHRLVPPPEETYSLHKKMGGSFLICSKLKARFPCKAMFEEAYSNYCKRQAQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.18346
R free: 0.25887
Average B factor: 76.273
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: One part of ADCK3 R611K, 0.2 mM, AMPPNP 2 mM, MgCl2, 4mM, mixed with an equal volume of sodium polyacrylate 5100, 26%; magnesium chloride, 20 mM; HEPES, 100 mM, pH 7.5
Matthews coefficient: 2.44
Solvent content (%): 49.61
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2016-08-17
Factor XIa in Complex with Compound 2f (PDB entry 7V12)
Macromolecule: Coagulation factor XIa light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.631
R work: 0.1835
R free: 0.2236
Average B factor: 21.6644
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 4000, 100mM Na Citrate pH 5.0
Matthews coefficient: 2.17
Solvent content (%): 43.3
Ligand: 5-[1-[(1~{R})-1-[5-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]-1-oxidanyl-pyridin-2-yl]-2-cyclopropyl-ethyl]pyrazol-4-yl]-6-fluoranyl-pyridin-2-amine (OR0)
Ligand formula: C25 H20 Cl F2 N9 O
Ligand molecular weight: 535.936
Ligand SMILES: c1cc([n+](cc1c2c(ccc(c2F)Cl)n3cnnn3)[O-])C(CC4CC4)n5cc(cn5)c6ccc(nc6F)N
Ligand InChI: InChI=1S/C25H20ClF2N9O/c26-18-5-7-20(36-13-30-33-34-36)23(24(18)27)15-3-6-19(37(38)12-15)21(9-14-1-2-14)35-11-16(10-31-35)17-4-8-22(29)32-25(17)28/h3-8,10-14,21H,1-2,9H2,(H2,29,32)/t21-/m1/s1
Release date: 2022-08-03
Structure of the IRAK4 kinase domain with compound 41 (PDB entry 6O95)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 320 residues
Sequence: MHHHHHHGENLYFQGSVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTASGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.188
R free: 0.217
Average B factor: 34.34
Crystallization method: VAPOR DIFFUSION
Crystal growth procedure: 2.6-2.9 M Ammonium Sulfate, Hepes
Matthews coefficient: 2.51
Solvent content (%): 51
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: 2019-05-22
Crystal Structure of human phosphodiesterase 10 in complex with 3-methylimidazo[4,5-f]quinolin-2-amine (PDB entry 5SG2)
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): 2.15
R work: 0.1851
R free: 0.2426
Average B factor: 45.32
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: 2.6
Solvent content (%): 52.65
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: 2022-10-12
Transglutaminase 2 - Intermediate State (PDB entry 9BC4)
Macromolecule: Protein-glutamine gamma-glutamyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.13
Sequence length: 687 residues
Sequence: MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVIIGPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.18625
R free: 0.2301
Average B factor: 25.782
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 15% PEG4K, 0.15 M Ammonium sulfate, 0.1 M HEPES (pH 7.0).
Matthews coefficient: 1.54
Solvent content (%): 20.21
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2024-07-03
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000446a (PDB entry 5QON)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.195
R free: 0.2521
Average B factor: 33.528
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.56
Solvent content (%): 51.87
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: 2019-05-08
FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-{3-[(2-phenylamino-5-trifluoromethyl-pyrimidin-4-ylamino)-methyl]-pyridin-2-yl}-methanesulfonamide (PDB entry 6YXV)
Macromolecule: Focal adhesion kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 282 residues
Sequence: GSGSTRDYEIQRERIELGRCIGEGQFGDVHQGIYMSPENPALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVITENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLGDFGLSRYMEDSTYYKASKGKLPIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILEEEKAQQEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.298
R work: 0.202
R free: 0.232
Average B factor: 60.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 15% PEG 3350
Matthews coefficient: 3.02
Solvent content (%): 59.29
Ligand: ~{N}-methyl-~{N}-[3-[(~{E})-[2-phenylazanyl-5-(trifluoromethyl)pyrimidin-4-yl]iminomethyl]pyridin-2-yl]methanesulfonamide (Q2H)
Ligand formula: C19 H17 F3 N6 O2 S
Ligand molecular weight: 450.437
Ligand SMILES: CN(c1c(cccn1)C=Nc2c(cnc(n2)Nc3ccccc3)C(F)(F)F)S(=O)(=O)C
Ligand InChI: InChI=1S/C19H17F3N6O2S/c1-28(31(2,29)30)17-13(7-6-10-23-17)11-24-16-15(19(20,21)22)12-25-18(27-16)26-14-8-4-3-5-9-14/h3-12H,1-2H3,(H,25,26,27)/b24-11+
Release date: 2021-02-10
Notum_Valsartan complex (PDB entry 7BM1)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.37
R work: 0.1836
R free: 0.2177
Average B factor: 24.7359
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 2.02
Solvent content (%): 39.1
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: 2022-03-02
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000203a (PDB entry 7FQZ)
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): 2.09
R work: 0.1665
R free: 0.2085
Average B factor: 47.765
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 (%): 62.72
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
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000055b (PDB entry 7GSR)
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): 1.69
R work: 0.1945
R free: 0.2248
Average B factor: 35.922
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.29
Solvent content (%): 62.61
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: 2024-01-24
Crystal structure of the bromodomain of human ATAD2 in complex with Compound A12 (PDB entry 5F36)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.169
R free: 0.1895
Average B factor: 35.3911
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5
Matthews coefficient: 4.08
Solvent content (%): 69.86
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: 2016-12-14
Crystal structure of MDM2 in complex with compound 13. (PDB entry 6I3S)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 94 residues
Sequence: QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1884
R free: 0.2392
Average B factor: 18.208
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.10 M (NH4)2SO4, 0.10 M Na acetate
Matthews coefficient: 2.25
Solvent content (%): 45.48
Ligand: (3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione (H28)
Ligand formula: C23 H18 Cl2 F N3 O2
Ligand molecular weight: 458.312
Ligand SMILES: c1cc(c(c(c1)Cl)F)C2C3C(C=NC3=O)N(C24c5ccc(cc5NC4=O)Cl)CC6CC6
Ligand InChI: InChI=1S/C23H18Cl2FN3O2/c24-12-6-7-14-16(8-12)28-22(31)23(14)19(13-2-1-3-15(25)20(13)26)18-17(9-27-21(18)30)29(23)10-11-4-5-11/h1-3,6-9,11,17-19H,4-5,10H2,(H,28,31)/t17-,18+,19-,23+/m0/s1
Release date: 2018-12-19
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000352a (PDB entry 5QI0)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.05
R work: 0.1355
R free: 0.1566
Average B factor: 12.816
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 2.01
Solvent content (%): 38.67
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: 2019-04-10
Crystal structure of an inactive state of GMPPNP-bound RhoA (PDB entry 6V6M)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 183 residues
Sequence: GSMAAIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.2126
R free: 0.2359
Average B factor: 19.8698
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 277
Crystal growth procedure: 20-24% PEG8K, 15% Dioxane, 0.1M Tris pH8.0
Matthews coefficient: 2.3
Solvent content (%): 46.61
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: 2020-12-09
The second sphere residue T263 is important for function and activity of PTP1B through modulating WPD loop (PDB entry 4QAP)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 299 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQNADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.903
R work: 0.209
R free: 0.242
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 8-24% (w/v) polyethylene glycol 4000, 100mM Hepes (pH 7.0), 200mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 3.39
Solvent content (%): 63.71
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: 2015-02-11
Human Angiogenin in complex with sulphate anions at a basic solution (PDB entry 5EPZ)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 120 residues
Sequence: DNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1833
R free: 0.21749
Average B factor: 19.759
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M Tris/HCl buffer pH 8.0, 2.4 M ammonium sulphate
Matthews coefficient: 2.38
Solvent content (%): 48.29
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: 2016-08-17
Structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06645342) (PDB entry 4W8E)
Macromolecule: Serine/threonine-protein kinase 24 36 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 291 residues
Sequence: GLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1748
R free: 0.2125
Average B factor: 46.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris-HCl (pH 8.5), 180mM MgCl2, 5mM Manganese acetate, 10-17% PEG3350
Matthews coefficient: 2.31
Solvent content (%): 46.75
Ligand: 3-{4-[(2R)-2-(5-methyl-1,2,4-oxadiazol-3-yl)morpholin-4-yl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile (3JB)
Ligand formula: C20 H17 N7 O2
Ligand molecular weight: 387.395
Ligand SMILES: Cc1nc(no1)C2CN(CCO2)c3c4c(c[nH]c4ncn3)c5cccc(c5)C#N
Ligand InChI: InChI=1S/C20H17N7O2/c1-12-25-18(26-29-12)16-10-27(5-6-28-16)20-17-15(9-22-19(17)23-11-24-20)14-4-2-3-13(7-14)8-21/h2-4,7,9,11,16H,5-6,10H2,1H3,(H,22,23,24)/t16-/m1/s1
Release date: 2015-03-18
Crystal structure of chimeric carbonic anhydrase XII with 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide (PDB entry 6YHC)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVEFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDAGKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.28
R work: 0.1304
R free: 0.1721
Average B factor: 21.824
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 2.04
Solvent content (%): 39.59
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: 2021-04-07