1nq5

Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ser Complexed With Nad+

Method: X-RAY DIFFRACTION Dmax: 109.0 Å Quality: GOOD

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

Glyceraldehyde 3-phosphate dehydrogenase

Geobacillus stearothermophilus

UniProt P00362

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 O; UniProt 1–334 Chain Q; UniProt 1–334 Mutation:C149S SO4 SULFATE ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG 4000, sodium acetate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.11 Å R-free 0.249
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–334 Chain C; UniProt 1–334 Mutation:C149S SO4 SULFATE ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG 4000, sodium acetate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.11 Å R-free 0.249
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–334 Chain C; UniProt 1–334 Mutation:C149S SO4 SULFATE ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG 4000, sodium acetate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.11 Å R-free 0.249

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.

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G3P_BACST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–334; UniProt 1–334 Author chain C; PDBConstruct 1–334; UniProt 1–334 Author chain O; PDBConstruct 1–334; UniProt 1–334 Author chain Q; PDBConstruct 1–334; UniProt 1–334

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 1nq5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nq5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nq5
Deposition date deposition_date2003-01-21
Structure title titleGlyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ser Complexed With Nad+
Keywords keywordsGlycolysis, Oxidoreductase, NAD; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.48
Radius of gyration Rg (electron density) rg_electron34.88
Forward intensity I(0) i0342135000.00
Molecular weight molecular_weight146730.0 kDa
Excluded volume excluded_volume182940 ų
Envelope volume envelope_volume240620 ų
Hydration-shell volume shell_volume56317 ų
Envelope diameter envelope_diameter111.6
Shell Rg shell_rg42.73
Envelope Rg envelope_rg34.02
Shape Rg shape_rg34.84
Total Rg total_rg35.57
Total atoms total_atoms10296
Residues n_residues1328
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax109.0
Rg (real space) rg_real35.29
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real3.4210e+08
I(0) uncertainty (real space) i0_real_error5.9690e+06
Rg (reciprocal space) rg_reciprocal35.41
I(0) (reciprocal space) i0_reciprocal342200000.0000
Solution quality estimate total_estimate0.8897
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.4
Skewness Skewness skewness0.121
Kurtosis Kurtosis kurtosis-0.459
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49280000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.789

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1nq5a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nq5a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd1nq5c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nq5c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd1nq5o1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nq5o2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd1nq5q1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1nq5q2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like

CATH v4.4 (8 domains)

Domain ID domain_id1nq5A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nq5A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1nq5C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nq5C02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1nq5O01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nq5O02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1nq5Q01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1nq5Q02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2

8. Citations (1)

9. Files and Curves (10)