5za0

A cryo-protectant induces the conformational change of glyceraldehyde-3-phosphate dehydrogenase

Method: X-RAY DIFFRACTION D_max: 70.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glyceraldehyde-3-phosphate dehydrogenase A

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Homooligomer Protein × 4 其他Polymer 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–331	Not recorded	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277.15 K；Ammonium sulfate, MES	Resolution 2.00 Å R-free 0.205

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 5ZA0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DC3 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–330（330 aa） Fragment：APO Chain B 1–330（330 aa） Fragment：APO	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, MAGNESIUM CHLORIDE, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.241
1DC3 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–330（330 aa） Fragment：APO Chain B 1–330（330 aa） Fragment：APO	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, MAGNESIUM CHLORIDE, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.241
1DC4 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–330（330 aa） Chain B 1–330（330 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	G3P SN-GLYCEROL-3-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, MAGNESIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.258
1DC4 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–330（330 aa） Chain B 1–330（330 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	G3P SN-GLYCEROL-3-PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, MAGNESIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.258
1DC5 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–330（330 aa） Fragment：APO Chain B 1–330（330 aa） Fragment：APO	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, MAGNESIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.281
1DC5 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–330（330 aa） Fragment：APO Chain B 1–330（330 aa） Fragment：APO	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, MAGNESIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.281
1DC6 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES. Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–330（330 aa） Fragment：HOLO Chain B 1–330（330 aa） Fragment：HOLO	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.291
1DC6 STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES. Deposited 1999-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–330（330 aa） Fragment：HOLO Chain B 1–330（330 aa） Fragment：HOLO	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.291
1GAD COMPARISON OF THE STRUCTURES OF WILD TYPE AND A N313T MUTANT OF ESCHERICHIA COLI GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASES: IMPLICATION FOR NAD BINDING AND COOPERATIVITY Deposited 1995-10-24	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 O 1–330（330 aa） Chain P 1–330（330 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1GAE COMPARISON OF THE STRUCTURES OF WILD TYPE AND A N313T MUTANT OF ESCHERICHIA COLI GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASES: IMPLICATION FOR NAD BINDING AND COOPERATIVITY Deposited 1995-10-24	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 O 1–330（330 aa） Chain P 1–330（330 aa）	Mutation：N313T Mutation：N313T	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.17 Å
1S7C Crystal structure of MES buffer bound form of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli Deposited 2004-01-29	Different construct 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 1–330（330 aa）	Not recorded	SO4 SULFATE ION × 20 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；2.4M ammonium sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.04 Å R-free 0.220
2VYN Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer Deposited 2008-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–331（331 aa） Chain B 1–331（331 aa） Chain C 1–331（331 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	FMT FORMIC ACID × 14 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.2M NA FORMATE, 20% PEG 3350, 0.1M HEPES PH 7.5	Resolution 2.20 Å R-free 0.224
2VYV Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer Deposited 2008-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–331（331 aa） Chain B 1–331（331 aa） Chain C 1–331（331 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	FMT FORMIC ACID × 14 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 1GP SN-GLYCEROL-1-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.2M NA FORMATE, 20% PEG 3350, 0.1M HEPES PH 7.5	Resolution 2.38 Å R-free 0.251
5O0V crystal structure of E. coli GAP-DH by fortuitous crystallization as an impurity from a solution of human liver FBPase Deposited 2017-05-17	Different construct 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 2–331（330 aa）	Not recorded	GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；unknown	Resolution 2.40 Å R-free 0.189
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain M 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain N 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain O 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO4 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 3–331（329 aa）	Mutation：D78G	AG SILVER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 3.10 Å R-free 0.240
6IO6 Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A at non-catalytic site Deposited 2018-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–331（329 aa）	Mutation：D79G	AG SILVER ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Malic acid, PEG3350 20%	Resolution 2.64 Å R-free 0.243
6IOJ Glyceraldehyde-3-phosphate dehydrogenase A (apo-form) Deposited 2018-10-30	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 3–331（329 aa）	Mutation：D79G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.15M Malic acid, PEG3350 25%	Resolution 2.29 Å R-free 0.221

13 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G3P1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–331； UniProt 1–331

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5za0
Deposition date deposition_date	2018-02-06
Structure title title	A cryo-protectant induces the conformational change of glyceraldehyde-3-phosphate dehydrogenase
Keywords keywords	HYPOTHETICAL, OXIDOREDUCTASE, cryo-protectant, glycolysis; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.09 Å
Radius of gyration Rg (electron density) rg_electron	20.27 Å
Forward intensity I(0) i0	21762700.00
Molecular weight molecular_weight	35275.0 kDa
Excluded volume excluded_volume	44086 Å³
Envelope volume envelope_volume	52395 Å³
Hydration-shell volume shell_volume	21607 Å³
Envelope diameter envelope_diameter	72.0 Å
Shell Rg shell_rg	26.65 Å
Envelope Rg envelope_rg	20.41 Å
Shape Rg shape_rg	20.29 Å
Total Rg total_rg	21.04 Å
Total atoms total_atoms	2479
Residues n_residues	330
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	70.7 Å
Rg (real space) rg_real	21.00 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.1760e+07
I(0) uncertainty (real space) i0_real_error	2.5610e+05
Rg (reciprocal space) rg_reciprocal	21.02 Å
I(0) (reciprocal space) i0_reciprocal	21760000.0000
Solution quality estimate total_estimate	0.8824
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.313
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4000000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Glyceraldehyde-3-phosphate dehydrogenase A
Molecular weight formula_weight	35577.4 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2649

MTIKVGINGFGRIGRIVFRAAQKRSDIEIVAINDLLDADYMAYMLKYDSTHGRFDGTVEVKDGHLIVNGKKIRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGYSNKVLDLIAHISK

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5za0a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d5za0a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

CATH v4.4 (1 domains)

Domain ID domain_id	5za0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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8. Citations (1)

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Unit-cell length a length_a	121.295 Å
Unit-cell length b length_b	121.295 Å
Unit-cell length c length_c	156.056 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	47.880 Å
R factor r_factor	0.1848
R_work r_work	0.1838
R_free r_free	0.2047

fit	/app/data/saxs_computation/za/5za0/5za0.fit
pddf	/app/data/pr_computation/za/5za0/5za0.pr.out
profile	/app/data/saxs_computation/za/5za0/5za0.dat