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Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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IF	>30 >20 >10 >5 all

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Structure paper

Title	An expanded trove of fragment-bound structures for the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data.
Journal, issue, pages	Structure, Vol. 32, Page 1231-1238.e4, Year 2024
Publish date	Jan 3, 2024 (structure data deposition date)
Authors	Mehlman, T. / Ginn, H.M. / Keedy, D.A.
External links	Structure / PubMed:38861991
Methods	X-ray diffraction
Resolution	1.51 - 2.47 Å
Structure data	PDB-7gs7: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000621a Method: X-RAY DIFFRACTION / Resolution: 1.66 Å PDB-7gs8: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000466a Method: X-RAY DIFFRACTION / Resolution: 1.67 Å PDB-7gs9: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000631a Method: X-RAY DIFFRACTION / Resolution: 1.96 Å PDB-7gsa: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000260a Method: X-RAY DIFFRACTION / Resolution: 1.72 Å PDB-7gsb: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000438a Method: X-RAY DIFFRACTION / Resolution: 1.72 Å PDB-7gsc: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000729a Method: X-RAY DIFFRACTION / Resolution: 1.69 Å PDB-7gsd: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000605a Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-7gse: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000383a Method: X-RAY DIFFRACTION / Resolution: 1.89 Å PDB-7gsf: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000421a Method: X-RAY DIFFRACTION / Resolution: 1.78 Å PDB-7gsg: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000316a Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-7gsh: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000530a Method: X-RAY DIFFRACTION / Resolution: 1.88 Å PDB-7gsi: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000046b Method: X-RAY DIFFRACTION / Resolution: 1.71 Å PDB-7gsj: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000543a Method: X-RAY DIFFRACTION / Resolution: 1.77 Å PDB-7gsk: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000279a Method: X-RAY DIFFRACTION / Resolution: 1.84 Å PDB-7gsl: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000274b Method: X-RAY DIFFRACTION / Resolution: 1.77 Å PDB-7gsm: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000437b Method: X-RAY DIFFRACTION / Resolution: 2.03 Å PDB-7gsn: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000519b Method: X-RAY DIFFRACTION / Resolution: 1.87 Å PDB-7gso: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000029a Method: X-RAY DIFFRACTION / Resolution: 1.72 Å PDB-7gsq: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000149a Method: X-RAY DIFFRACTION / Resolution: 1.73 Å PDB-7gsr: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000055b Method: X-RAY DIFFRACTION / Resolution: 1.69 Å PDB-7gst: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000056a Method: X-RAY DIFFRACTION / Resolution: 1.64 Å PDB-7gsu: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000382a Method: X-RAY DIFFRACTION / Resolution: 1.65 Å PDB-7gsv: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000830b Method: X-RAY DIFFRACTION / Resolution: 1.92 Å PDB-7gsw: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000422b Method: X-RAY DIFFRACTION / Resolution: 1.79 Å PDB-7gsx: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001440b Method: X-RAY DIFFRACTION / Resolution: 1.67 Å PDB-7gsy: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001175b Method: X-RAY DIFFRACTION / Resolution: 1.97 Å PDB-7gsz: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000686b Method: X-RAY DIFFRACTION / Resolution: 1.91 Å PDB-7gt0: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000275a Method: X-RAY DIFFRACTION / Resolution: 1.76 Å PDB-7gt1: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000209a Method: X-RAY DIFFRACTION / Resolution: 1.91 Å PDB-7gt2: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000752b Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-7gt3: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000527a Method: X-RAY DIFFRACTION / Resolution: 1.59 Å PDB-7gt4: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000528a Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-7gt5: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000529a Method: X-RAY DIFFRACTION / Resolution: 1.61 Å PDB-7gt6: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000530a Method: X-RAY DIFFRACTION / Resolution: 1.66 Å PDB-7gt7: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001181b Method: X-RAY DIFFRACTION / Resolution: 1.84 Å PDB-7gt8: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001439b Method: X-RAY DIFFRACTION / Resolution: 1.91 Å PDB-7gt9: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000463b Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-7gta: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000065a Method: X-RAY DIFFRACTION / Resolution: 2.06 Å PDB-7gtb: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000899b Method: X-RAY DIFFRACTION / Resolution: 1.86 Å PDB-7gtc: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00001145b Method: X-RAY DIFFRACTION / Resolution: 1.92 Å PDB-7gtd: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000110a Method: X-RAY DIFFRACTION / Resolution: 1.91 Å PDB-7gte: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000646b Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-7gtf: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000754b Method: X-RAY DIFFRACTION / Resolution: 1.97 Å PDB-7gtg: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000684a Method: X-RAY DIFFRACTION / Resolution: 1.69 Å PDB-7gth: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000637a Method: X-RAY DIFFRACTION / Resolution: 1.66 Å PDB-7gti: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000571a Method: X-RAY DIFFRACTION / Resolution: 1.66 Å PDB-7gtj: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000280c Method: X-RAY DIFFRACTION / Resolution: 1.83 Å PDB-7gtk: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000552a Method: X-RAY DIFFRACTION / Resolution: 1.76 Å PDB-7gtl: PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000554a Method: X-RAY DIFFRACTION / Resolution: 1.83 Å PDB-7gtm: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000543a Method: X-RAY DIFFRACTION / Resolution: 1.72 Å PDB-7gtn: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000625a Method: X-RAY DIFFRACTION / Resolution: 1.66 Å PDB-7gto: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000602a Method: X-RAY DIFFRACTION / Resolution: 1.65 Å PDB-7gtp: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000688a Method: X-RAY DIFFRACTION / Resolution: 2.47 Å PDB-7gtq: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000311a Method: X-RAY DIFFRACTION / Resolution: 2.09 Å PDB-7gtr: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000587a Method: X-RAY DIFFRACTION / Resolution: 1.78 Å PDB-7gts: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000604a Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-7gtt: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000148a Method: X-RAY DIFFRACTION / Resolution: 1.93 Å PDB-7gtu: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000297a Method: X-RAY DIFFRACTION / Resolution: 2.08 Å PDB-7gtv: PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000765c Method: X-RAY DIFFRACTION / Resolution: 1.72 Å PDB-7gtw: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster1 Method: X-RAY DIFFRACTION / Resolution: 1.51 Å PDB-7gtx: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster2 Method: X-RAY DIFFRACTION / Resolution: 1.51 Å PDB-7gty: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster3 Method: X-RAY DIFFRACTION / Resolution: 1.54 Å PDB-7gtz: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster5 Method: X-RAY DIFFRACTION / Resolution: 1.6 Å PDB-7gu0: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster6 Method: X-RAY DIFFRACTION / Resolution: 1.66 Å PDB-7gu1: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster7 Method: X-RAY DIFFRACTION / Resolution: 1.59 Å PDB-7gu2: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster8 Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-7gu3: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster9 Method: X-RAY DIFFRACTION / Resolution: 1.74 Å PDB-7gu4: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster11 Method: X-RAY DIFFRACTION / Resolution: 1.59 Å PDB-7gu5: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster12 Method: X-RAY DIFFRACTION / Resolution: 1.52 Å PDB-7gu6: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster14 Method: X-RAY DIFFRACTION / Resolution: 1.56 Å PDB-7gu7: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster15 Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-7gu8: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster16 Method: X-RAY DIFFRACTION / Resolution: 1.59 Å PDB-7gu9: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster17 Method: X-RAY DIFFRACTION / Resolution: 1.53 Å PDB-7gua: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster18 Method: X-RAY DIFFRACTION / Resolution: 1.63 Å PDB-7gub: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster19 Method: X-RAY DIFFRACTION / Resolution: 1.94 Å PDB-7guc: PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster20 Method: X-RAY DIFFRACTION / Resolution: 1.78 Å
Chemicals	ChemComp-TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH bufferYM ChemComp-RU4: 4-(1,2,3-thiadiazol-4-yl)phenyl ethylcarbamate ChemComp-HOH: WATER ChemComp-GV1: ~{N},~{N},5,6-tetramethylthieno[2,3-d]pyrimidin-4-amine ChemComp-LV7: ~{N}-[2-(aminocarbamoyl)phenyl]ethanamide PDB-1aa6: REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI PDB-1aa7: INFLUENZA VIRUS MATRIX PROTEIN CRYSTAL STRUCTURE AT PH 4.0 ChemComp-WLJ: (azepan-1-yl)(2,6-difluorophenyl)methanone ChemComp-GVY: 4-(5-amino-1,3,4-thiadiazol-2-yl)phenol ChemComp-T1J: 2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol ChemComp-B0Y: 5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamide ChemComp-RZG: methyl 4-sulfamoylbenzoate ChemComp-WLY: 2-(4-methylphenyl)-N-{[(2S)-oxolan-2-yl]methyl}acetamide ChemComp-LWV: 2-morpholin-4-ylaniline ChemComp-B0G: (phenylmethyl) 4-oxidanylpiperidine-1-carboxylate ChemComp-UXG: 1-(diphenylmethyl)azetidin-3-ol PDB Unreleased entry PDB-1aa8: Unknown entry PDB-1abb: CONTROL OF PHOSPHORYLASE B CONFORMATION BY A MODIFIED COFACTOR: CRYSTALLOGRAPHIC STUDIES ON R-STATE GLYCOGEN PHOSPHORYLASE RECONSTITUTED WITH PYRIDOXAL 5'-DIPHOSPHATE ChemComp-R7T: 4-[(thiophen-2-yl)methyl]benzoic acid PDB-1aba: THE STRUCTURE OF OXIDIZED BACTERIOPHAGE T4 GLUTAREDOXIN (THIOREDOXIN). REFINEMENT OF NATIVE AND MUTANT PROTEINS ChemComp-JKY: N-[(4-chlorophenyl)methyl]methanesulfonamide PDB-1aa9: HUMAN C-HA-RAS(1-171)(DOT)GDP, NMR, MINIMIZED AVERAGE STRUCTURE PDB-1abc: Unknown entry ChemComp-I8M: 2-[(morpholin-4-yl)methyl]phenol PDB-1abd: Unknown entry PDB-1abe: NOVEL STEREOSPECIFICITY OF THE L-ARABINOSE-BINDING PROTEIN ChemComp-JLM: 3-methyl-1-benzofuran-2-carboxylic acid PDB-1abf: SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES ChemComp-WFI: 1-[4-methyl-2-(pyridin-4-yl)-1,3-thiazol-5-yl]methanamine PDB-1abg: Unknown entry PDB Unreleased entry PDB-1abh: Unknown entry ChemComp-JNG: [(4-chlorophenyl)sulfanyl]acetic acid PDB-1abi: STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS PDB-1abj: STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS PDB Unreleased entry PDB-1abk: Unknown entry PDB Unreleased entry PDB-1ack: Unknown entry PDB-1abl: Unknown entry ChemComp-8K2: 5-chloranylthiophene-2-sulfonamide PDB-1abr: CRYSTAL STRUCTURE OF ABRIN-A PDB-1abq: CRYSTAL STRUCTURE OF THE UNLIGANDED ABL TYROSINE KINASE SH3 DOMAIN ChemComp-4ZV: 1H-indole-5-carboxylic acid ChemComp-LVD: 1-phenylmethoxyurea PDB Unreleased entry PDB-1abp: Unknown entry PDB-1abo: CRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 DOMAIN WITH 3BP-1 SYNTHETIC PEPTIDE ChemComp-9EW: 1,2-benzoxazol-3-ol PDB-1abn: THE CRYSTAL STRUCTURE OF THE ALDOSE REDUCTASE NADPH BINARY COMPLEX PDB Unreleased entry PDB-1abm: Unknown entry PDB-1aby: CYANOMET RHB1.1 (RECOMBINANT HEMOGLOBIN) ChemComp-JP4: [2-(morpholin-4-yl)phenyl]methanol PDB Unreleased entry PDB-1abx: Unknown entry PDB-1abw: DEOXY RHB1.1 (RECOMBINANT HEMOGLOBIN) PDB-1abv: N-TERMINAL DOMAIN OF THE DELTA SUBUNIT OF THE F1F0-ATP SYNTHASE FROM ESCHERICHIA COLI, NMR, MINIMIZED AVERAGE STRUCTURE PDB-1abu: Unknown entry PDB-1abt: NMR SOLUTION STRUCTURE OF AN ALPHA-BUNGAROTOXIN(SLASH)NICOTINIC RECEPTOR PEPTIDE COMPLEX ChemComp-W1D: (4-acetylphenoxy)acetic acid ChemComp-S7S: ~{N}-(2-ethyl-1,2,3,4-tetrazol-5-yl)butanamide ChemComp-TAH: 2-(benzyloxy)benzohydrazide ChemComp-WZY: N-(4-methoxyphenyl)glycinamide PDB-1abs: PHOTOLYSED CARBONMONOXY-MYOGLOBIN AT 20 K ChemComp-8YM: 2-[(2-acetylphenyl)sulfanyl]benzoic acid ChemComp-UJQ*: 9~{H}-xanthene-9-carboxylic acid
Source	homo sapiens (human)
Keywords	HYDROLASE / PanDDA / Diamond I04-1 fragment screening / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multiconformer

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