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1dru

ESCHERICHIA COLI DHPR/NADH COMPLEX

Method: X-RAY DIFFRACTION Dmax: 72.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DIHYDRODIPICOLINATE REDUCTASE

Escherichia coli

UniProt P04036

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 1–273 Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5 Resolution 2.20 Å

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 1DRU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ARZ ESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX WITH NADH AND 2,6 PYRIDINE DICARBOXYLATE Deposited 1997-08-08 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 1–273（273 aa）
Chain B 1–273（273 aa）
Chain C 1–273（273 aa）
Chain D 1–273（273 aa）
Not recorded PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 2 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 3 PDC PYRIDINE-2,6-DICARBOXYLIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 23-26% PEG 8000, IN 160-180 MM POTASSIUM PHOSPHATE, 100 MM SODIUM CACODYLATE PH 7.5
Resolution 2.60 Å R-free 0.297
1DIH THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE Deposited 1994-09-14 Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–273（273 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1DRV ESCHERICHIA COLI DHPR/ACNADH COMPLEX Deposited 1996-06-28 Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–273（273 aa）
Not recorded A3D 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2.2 M (NH4)2SO4 IN 100 MM HEPES, PH=7.5
Resolution 2.20 Å
1DRW ESCHERICHIA COLI DHPR/NHDH COMPLEX Deposited 1996-06-28 Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–273（273 aa）
Not recorded NHD NICOTINAMIDE PURIN-6-OL-DINUCLEOTIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2.2M (NH4)2SO4 IN 100 MM HEPES, PH 7.5
Resolution 2.20 Å

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

View Construct and Data Evidence
UniProt name DAPB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–273； UniProt 1–273

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 1dru

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dru
Deposition date deposition_date1996-06-28
Structure title titleESCHERICHIA COLI DHPR/NADH COMPLEX
Keywords keywordsOXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier21.27 Å
Radius of gyration Rg (electron density) rg_electron20.34 Å
Forward intensity I(0) i015902200.00
Molecular weight molecular_weight28775.0 kDa
Excluded volume excluded_volume35493 ų
Envelope volume envelope_volume42944 ų
Hydration-shell volume shell_volume18350 ų
Envelope diameter envelope_diameter72.4 Å
Shell Rg shell_rg26.08 Å
Envelope Rg envelope_rg20.61 Å
Shape Rg shape_rg20.36 Å
Total Rg total_rg21.05 Å
Total atoms total_atoms2018
Residues n_residues270
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 dmax72.1 Å
Rg (real space) rg_real21.32 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real1.5900e+07
I(0) uncertainty (real space) i0_real_error2.0920e+05
Rg (reciprocal space) rg_reciprocal21.31 Å
I(0) (reciprocal space) i0_reciprocal15900000.0000
Solution quality estimate total_estimate0.7213
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.441
Kurtosis Kurtosis kurtosis-0.224
Angular range angular_range— – 0.3750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2818000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.946; Smooth: 0.915
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1drua1
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_idd1drua2
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.81.1.3 — Dihydrodipicolinate reductase-like

CATH v4.4 (2 domains)

Domain ID domain_id1druA01
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_id1druA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
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8. Citations (3)

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9. Files and Curves (10)