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6d43

CHARACTERIZATION OF HUMAN TRIOSEPHOSPHATE ISOMERASE S-NITROSYLATION

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Triosephosphate isomerase

Homo sapiens

UniProt P60174

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 41–286 Chain B； UniProt 41–286 Non-standard monomer：Yes (specific site not provided by mmCIF) IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；283 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol Resolution 2.04 Å R-free 0.256

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6D43 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HTI CRYSTAL STRUCTURE OF RECOMBINANT HUMAN TRIOSEPHOSPHATE ISOMERASE AT 2.8 ANGSTROMS RESOLUTION. TRIOSEPHOSPHATE ISOMERASE RELATED HUMAN GENETIC DISORDERS AND COMPARISON WITH THE TRYPANOSOMAL ENZYME Deposited 1994-10-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–248（248 aa）
Chain B 1–248（248 aa）
Not recorded PGA 2-PHOSPHOGLYCOLIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1WYI human triosephosphate isomerase of new crystal form Deposited 2005-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–248（248 aa）
Chain B 1–248（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions gel-tube under microgavity；pH 8；293 K；PEG4000, MgCl2, pH 8.0, gel-tube under microgavity, temperature 293K
Resolution 2.20 Å R-free 0.296
1WYI human triosephosphate isomerase of new crystal form Deposited 2005-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–248（248 aa）
Chain B 1–248（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions gel-tube under microgavity；pH 8；293 K；PEG4000, MgCl2, pH 8.0, gel-tube under microgavity, temperature 293K
Resolution 2.20 Å R-free 0.296
2IAM Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR Deposited 2006-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 22–36（15 aa） Fragment：residues 23-37 (22-36)
Mutation：T28I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；8% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.279
2IAN Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR Deposited 2006-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 22–36（15 aa） Fragment：residues 23-37 (22-36)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；10% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.296
2IAN Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR Deposited 2006-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 22–36（15 aa） Fragment：residues 23-37 (22-36)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；10% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.296
2IAN Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR Deposited 2006-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain M 22–36（15 aa） Fragment：residues 23-37 (22-36)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；10% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.296
2IAN Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR Deposited 2006-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 22–36（15 aa） Fragment：residues 23-37 (22-36)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；10% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.296
2JK2 STRUCTURAL BASIS OF HUMAN TRIOSEPHOSPHATE ISOMERASE DEFICIENCY. CRYSTAL STRUCTURE OF THE WILD TYPE ENZYME. Deposited 2008-06-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–249（248 aa） Fragment：RESIDUES 2-249
Chain B 2–249（248 aa） Fragment：RESIDUES 2-249
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；100 MM TRIS PH 8.5, 20% PEG MME2000, 10 MM NICL2
Resolution 1.70 Å R-free 0.252
2VOM Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and correlation to solvent perturbation. Deposited 2008-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–249（248 aa） Fragment：RESIDUES 2-249
Chain B 2–249（248 aa） Fragment：RESIDUES 2-249
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；100 MM TRIS PH 8.5, 20% PEG MME2000, 4% POLYPROPYLENE GLYCOL P400, 10 MM NICL2
Resolution 1.85 Å R-free 0.253
2VOM Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and correlation to solvent perturbation. Deposited 2008-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 2–249（248 aa） Fragment：RESIDUES 2-249
Chain D 2–249（248 aa） Fragment：RESIDUES 2-249
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；100 MM TRIS PH 8.5, 20% PEG MME2000, 4% POLYPROPYLENE GLYCOL P400, 10 MM NICL2
Resolution 1.85 Å R-free 0.253
4BR1 Protease-induced heterodimer of human triosephosphate isomerase. Deposited 2013-06-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 41–286（246 aa）
Chain B 41–286（246 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；100 MM TRIS PH 8.5, 30% POLYETHYLENE GLYCOL 4000, 200 MM SODIUM ACETATE TRIHYDRATE
Resolution 1.90 Å R-free 0.217
4E41 Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4 Deposited 2012-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 60–74（15 aa） Fragment：unp residues 60-74
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；20% (wt/vol) polyethylene glycol 1000, 0.2 M calcium acetate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 298K
Resolution 2.60 Å R-free 0.264
4E41 Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4 Deposited 2012-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 60–74（15 aa） Fragment：unp residues 60-74
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；20% (wt/vol) polyethylene glycol 1000, 0.2 M calcium acetate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 298K
Resolution 2.60 Å R-free 0.264
4POC Structure of Triosephosphate Isomerase Wild Type human enzyme. Deposited 2014-02-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–286（249 aa）
Chain B 38–286（249 aa）
Not recorded K POTASSIUM ION × 2 NA SODIUM ION × 1 BR BROMIDE ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；35% PEG 2000 MME, 0.05 KBr, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.187
4POD Structure of Triosephosphate Isomerase I170V mutant human enzyme. Deposited 2014-02-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–286（249 aa）
Chain B 38–286（249 aa）
Mutation：I170V Mutation：I170V K POTASSIUM ION × 2 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1 BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；34% PEG 2000 MME, 0.05 KBr, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.99 Å R-free 0.213
4UNK Crystal structure of human triosephosphate isomerase (mutant N15D) Deposited 2014-05-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 39–286（248 aa） Fragment：RESIDUES 39-286
Chain B 39–286（248 aa） Fragment：RESIDUES 39-286
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；200 MM AMMONIUM ACETATE, 100 MM TRIS PH 8.5, 25% V/VW/V POLYETHYLENE GLYCOL 3350
Resolution 2.00 Å R-free 0.224
4UNL Crystal structure of a single mutant (N71D) of triosephosphate isomerase from human Deposited 2014-05-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 39–286（248 aa） Fragment：RESIDUES 39-286
Chain B 39–286（248 aa） Fragment：RESIDUES 39-286
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；PROTEIN WAS CRYSTALLIZED FROM: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4,000
Resolution 1.50 Å R-free 0.226
4ZVJ Structure of human triose phosphate isomerase K13M Deposited 2015-05-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–286（249 aa）
Chain B 38–286（249 aa）
Mutation：K13M Mutation：K13M NA SODIUM ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；35% PEG 2000 MME, 50 mM KBr, Tris pH 7.5
Resolution 1.70 Å R-free 0.187
6C2G Human triosephosphate isomerase mutant V231M Deposited 2018-01-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–286（249 aa）
Chain C 38–286（249 aa）
Mutation：V231M Mutation：V231M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000.
Resolution 2.30 Å R-free 0.226
6C2G Human triosephosphate isomerase mutant V231M Deposited 2018-01-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 38–286（249 aa）
Chain D 38–286（249 aa）
Mutation：V231M Mutation：V231M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000.
Resolution 2.30 Å R-free 0.226
6NLH Structure of human triose phosphate isomerase R189A Deposited 2019-01-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 42–286（245 aa）
Chain E 42–286（245 aa）
Mutation：R189A Mutation：R189A NA SODIUM ION × 4 BR BROMIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；31% PEG 3350, 50 mM Potassium Bromide, Tris pH7.5
Resolution 2.20 Å R-free 0.216
6NLH Structure of human triose phosphate isomerase R189A Deposited 2019-01-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 42–286（245 aa）
Chain C 42–286（245 aa）
Mutation：R189A Mutation：R189A NA SODIUM ION × 7 BR BROMIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；31% PEG 3350, 50 mM Potassium Bromide, Tris pH7.5
Resolution 2.20 Å R-free 0.216
6NLH Structure of human triose phosphate isomerase R189A Deposited 2019-01-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 42–286（245 aa）
Chain F 42–286（245 aa）
Mutation：R189A Mutation：R189A NA SODIUM ION × 5 BR BROMIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；31% PEG 3350, 50 mM Potassium Bromide, Tris pH7.5
Resolution 2.20 Å R-free 0.216
6NLH Structure of human triose phosphate isomerase R189A Deposited 2019-01-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 42–286（245 aa）
Chain H 42–286（245 aa）
Mutation：R189A Mutation：R189A NA SODIUM ION × 4 BR BROMIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；31% PEG 3350, 50 mM Potassium Bromide, Tris pH7.5
Resolution 2.20 Å R-free 0.216
6UP1 Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure Deposited 2019-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 39–286（248 aa）
Chain B 39–286（248 aa）
Not recorded IPA ISOPROPYL ALCOHOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283.15 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Resolution 1.83 Å R-free 0.261
6UP5 Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure Deposited 2019-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 39–286（248 aa）
Chain B 39–286（248 aa）
Not recorded GOL GLYCEROL × 3 IPA ISOPROPYL ALCOHOL × 3 PGA 2-PHOSPHOGLYCOLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Resolution 1.92 Å R-free 0.232
6UP8 Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure Deposited 2019-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 39–286（248 aa）
Chain B 39–286（248 aa）
Mutation：F240L Mutation：F240L IPA ISOPROPYL ALCOHOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Resolution 2.00 Å R-free 0.253
6UPF Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure Deposited 2019-10-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 39–286（248 aa）
Chain B 39–286（248 aa）
Mutation：F240L Mutation：F240L PGA 2-PHOSPHOGLYCOLIC ACID × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.05 M Tris-HCl pH 7.5, 0.05 M NaCl, 1 mM EDTA, 15% PEG 4000 and 2 mM 2-PG
Resolution 1.65 Å R-free 0.197
7RDE Human Triose Phosphate Isomerase Q181P Deposited 2021-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–249（249 aa）
Chain B 1–249（249 aa）
Mutation：Q181P Mutation：Q181P BR BROMIDE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；30% PEG 3350, 50mM Potassium Bromide, Tris pH7.5
Resolution 1.31 Å R-free 0.162
7SX1 human triosephosphate isomerase mutant v154m Deposited 2021-11-22 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–249（249 aa）
Chain B 1–249（249 aa）
Mutation：V154M Mutation：V154M IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Resolution 2.23 Å R-free 0.225
7T0Q human triosephosphate isomerase mutant v154m Deposited 2021-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–249（248 aa）
Chain B 2–249（248 aa）
Mutation：V154M Mutation：V154M PGA 2-PHOSPHOGLYCOLIC ACID × 1 GOL GLYCEROL × 2 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Resolution 2.00 Å R-free 0.206
7UXB Human triosephosphate isomerase mutant G122R Deposited 2022-05-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–249（249 aa）
Chain B 1–249（249 aa）
Mutation：G122R Mutation：G122R IPA ISOPROPYL ALCOHOL × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol
Resolution 2.00 Å R-free 0.228
7UXV human triosephosphate isomerase mutant G122R Deposited 2022-05-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–249（249 aa）
Chain B 1–249（249 aa）
Mutation：G122R Mutation：G122R PGA 2-PHOSPHOGLYCOLIC ACID × 2 GOL GLYCEROL × 4 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-porpanol
Resolution 2.15 Å R-free 0.246
9F69 Crystal structure of human triose phosphate isomerase with methyl malonic acid ligand Deposited 2024-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–249（245 aa）
Not recorded DXX METHYLMALONIC ACID × 2 BR BROMIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl. Reservoir: 0.14 M KBr, 24% PEG 2000 MME. Hanging drop: 1.5:1.5:1.0 ul - Reservoir-Protein (8 mg/ml)-Seed stock. Cryoprotectant = 20% glycerol; Ligand soaking performed for 5-6 min in a mixture containing 24 mM methylmalonate (pH adjusted to 7.4), mother liquor, and cryo-protectant Ligand soaking and cryoprotectant were performed simultaneously
Resolution 1.17 Å R-free 0.184
9FFC Crystal structure of human triose phosphate isomerase with glycerol-3-phosphate ligand Deposited 2024-05-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–249（249 aa）
Not recorded G3P SN-GLYCEROL-3-PHOSPHATE × 2 BR BROMIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl. Reservoir: 0.14 M KBr, 24% PEG 2000 MME. Hanging drop: 1.5:1.5:1.0 ul - Reservoir-Protein (8 mg/ml)-Seed stock. Cryoprotectant = 20% glycerol; Ligand soaking performed for 5-6 min in a mixture containing 20 mM glycerol-3-phosphate (pH adjusted to 7.4), mother liquor, and cryo-protectant Ligand soaking and cryoprotectant were performed simultaneously
Resolution 1.25 Å R-free 0.180

26 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TPIS_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–246； UniProt 41–286 Author chain B； PDBConstruct 1–246； UniProt 41–286

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6d43

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6d43
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6d43
Deposition date deposition_date2018-04-17
Structure title titleCHARACTERIZATION OF HUMAN TRIOSEPHOSPHATE ISOMERASE S-NITROSYLATION
Keywords keywordsS-nitrosylation, isomerase, glycolysis, TIM-barrel, Dihydroxyacetone phosphate; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.14 Å
Radius of gyration Rg (electron density) rg_electron24.21 Å
Forward intensity I(0) i045815300.00
Molecular weight molecular_weight52711.0 kDa
Excluded volume excluded_volume66199 ų
Envelope volume envelope_volume76838 ų
Hydration-shell volume shell_volume26776 ų
Envelope diameter envelope_diameter80.0 Å
Shell Rg shell_rg31.46 Å
Envelope Rg envelope_rg24.39 Å
Shape Rg shape_rg24.22 Å
Total Rg total_rg25.03 Å
Total atoms total_atoms3710
Residues n_residues490
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.8 Å
Rg (real space) rg_real25.18 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real4.5820e+07
I(0) uncertainty (real space) i0_real_error5.6960e+05
Rg (reciprocal space) rg_reciprocal25.17 Å
I(0) (reciprocal space) i0_reciprocal45810000.0000
Solution quality estimate total_estimate0.8863
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5 Å
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.424
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14760000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.829
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6d43a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.1 — Triosephosphate isomerase (TIM)
Family Family familyc.1.1.1 — Triosephosphate isomerase (TIM)
Domain ID domain_idd6d43b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.1 — Triosephosphate isomerase (TIM)
Family Family familyc.1.1.1 — Triosephosphate isomerase (TIM)

CATH v4.4 (2 domains)

Domain ID domain_id6d43A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id6d43B00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
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8. Citations (1)

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9. Files and Curves (10)