1ihx

Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry

Method: X-RAY DIFFRACTION D_max: 94.4 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–333 Chain B； UniProt 1–333 Chain C； UniProt 1–333 Chain D； UniProt 1–333	Not recorded	SO4 SULFATE ION × 8 SND THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.1；298 K；ammonium sulphate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.204

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 1IHX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CRW CRYSTAL STRUCTURE OF APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR AT 2.0A RESOLUTION Deposited 1999-08-16	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 G 1–333（333 aa） Chain R 1–333（333 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；291 K；pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 18K	Resolution 2.00 Å R-free 0.226
1DSS STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR Deposited 1997-06-04	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 G 1–333（333 aa） Fragment：NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN Chain R 1–333（333 aa） Fragment：NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；290 K；THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULFATE IN 0.1M PHOSPHATE BUFFER(PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULFATE IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C., temperature 290K	Resolution 1.88 Å R-free 0.218
1IHY GAPDH complexed with ADP-ribose Deposited 2001-04-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–333（333 aa） Chain B 1–333（333 aa） Chain C 1–333（333 aa） Chain D 1–333（333 aa）	Not recorded	SO4 SULFATE ION × 8 APR ADENOSINE-5-DIPHOSPHORIBOSE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；ammonium sulphate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.207
1SZJ STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION Deposited 1997-02-04	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 G 1–333（333 aa） Fragment：NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN Chain R 1–333（333 aa） Fragment：NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；280 K；THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULPHATE IN 0.1M PHOSPHATE BUFFER (PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULPHATE IN SAME BUFFER. THE CRYSTALLIZATION WAS CARRIED OUT AT 280K.	Resolution 2.00 Å R-free 0.223

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G3P_PALVE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–333； UniProt 1–333 Author chain B； PDBConstruct 1–333； UniProt 1–333 Author chain C； PDBConstruct 1–333； UniProt 1–333 Author chain D； PDBConstruct 1–333； UniProt 1–333

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	1ihx
Deposition date deposition_date	2001-04-20
Structure title title	Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry
Keywords keywords	GAPDH, asymmetry, SNAD, 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	32.56 Å
Radius of gyration Rg (electron density) rg_electron	32.00 Å
Forward intensity I(0) i0	336445000.00
Molecular weight molecular_weight	146490.0 kDa
Excluded volume excluded_volume	182980 Å³
Envelope volume envelope_volume	217960 Å³
Hydration-shell volume shell_volume	53858 Å³
Envelope diameter envelope_diameter	100.7 Å
Shell Rg shell_rg	40.99 Å
Envelope Rg envelope_rg	32.04 Å
Shape Rg shape_rg	32.01 Å
Total Rg total_rg	32.65 Å
Total atoms total_atoms	10248
Residues n_residues	1332
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	94.4 Å
Rg (real space) rg_real	32.29 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	3.3640e+08
I(0) uncertainty (real space) i0_real_error	4.5400e+06
Rg (reciprocal space) rg_reciprocal	32.40 Å
I(0) (reciprocal space) i0_reciprocal	336500000.0000
Solution quality estimate total_estimate	0.9000
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.066
Kurtosis Kurtosis kurtosis	-0.553
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	253700000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.814

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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
Molecular weight formula_weight	35855.1 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10476

SKIGINGFGRIGRLVLRTALEMGAQVVAVNDPFIALEYMVYMFKYDSTHGMFKGEVKVEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVIISAPSADAPMFVCGVNLEKYSKDMKVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLIKHMQKVDSA

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	679.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	228

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ihxa1
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	d1ihxa2
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	d1ihxb1
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	d1ihxb2
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	d1ihxc1
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	d1ihxc2
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	d1ihxd1
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	d1ihxd2
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 (8 domains)

Domain ID domain_id	1ihxA01
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	1ihxA02
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	1ihxB01
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	1ihxB02
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	1ihxC01
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	1ihxC02
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	1ihxD01
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	1ihxD02
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 (2)

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Unit-cell length a length_a	153.409 Å
Unit-cell length b length_b	100.506 Å
Unit-cell length c length_c	128.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.49 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.840 Å
R factor r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.2040

fit	/app/data/saxs_computation/ih/1ihx/1ihx.fit
pddf	/app/data/pr_computation/ih/1ihx/1ihx.pr.out
profile	/app/data/saxs_computation/ih/1ihx/1ihx.dat