1dc5

STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES

Method: X-RAY DIFFRACTION D_max: 89.2 Å Quality: EXCELLENT

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

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

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	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–330 Chain B； UniProt 1–330	Fragment：APO	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–330 Chain B； UniProt 1–330	Fragment：APO	No other associated polymer	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

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 1DC5	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 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 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 ligand/ion 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 ligand/ion 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
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 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 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 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 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 mutation/modification 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 mutation/modification 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
5ZA0 A cryo-protectant induces the conformational change of glyceraldehyde-3-phosphate dehydrogenase Deposited 2018-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–331（331 aa）	Not recorded	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
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 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 31 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 1–330； UniProt 1–330 Author chain B； PDBConstruct 1–330； UniProt 1–330

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	1dc5
Deposition date deposition_date	1999-11-04
Structure title title	STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES
Keywords keywords	GAPDH, SUBSTRATE, OXIDOREDUCTASE; 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	28.75 Å
Radius of gyration Rg (electron density) rg_electron	28.06 Å
Forward intensity I(0) i0	82321300.00
Molecular weight molecular_weight	70801.0 kDa
Excluded volume excluded_volume	88665 Å³
Envelope volume envelope_volume	110080 Å³
Hydration-shell volume shell_volume	32479 Å³
Envelope diameter envelope_diameter	89.8 Å
Shell Rg shell_rg	35.39 Å
Envelope Rg envelope_rg	27.65 Å
Shape Rg shape_rg	28.05 Å
Total Rg total_rg	28.83 Å
Total atoms total_atoms	4976
Residues n_residues	660
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	89.2 Å
Rg (real space) rg_real	28.68 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	8.2320e+07
I(0) uncertainty (real space) i0_real_error	1.1740e+06
Rg (reciprocal space) rg_reciprocal	28.71 Å
I(0) (reciprocal space) i0_reciprocal	82320000.0000
Solution quality estimate total_estimate	0.9124
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.208
Kurtosis Kurtosis kurtosis	-0.597
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13160000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dc5a1
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	d1dc5a2
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

Domain ID domain_id	d1dc5b1
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	d1dc5b2
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 (4 domains)

Domain ID domain_id	1dc5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1dc5A02
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

Domain ID domain_id	1dc5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1dc5B02
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	81.870 Å
Unit-cell length b length_b	134.540 Å
Unit-cell length c length_c	68.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2100
R_work r_work	0.2060
R_free r_free	0.2810

Description description	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Molecular weight formula_weight	35446.2 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5206

STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES

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

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

fit	/app/data/saxs_computation/dc/1dc5/1dc5.fit
pddf	/app/data/pr_computation/dc/1dc5/1dc5.pr.out
profile	/app/data/saxs_computation/dc/1dc5/1dc5.dat