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2egh

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with a magnesium ion, NADPH and fosmidomycin

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

1-deoxy-D-xylulose 5-phosphate reductoisomerase

Escherichia coli str. K12 substr.

UniProt P45568

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 MAGNESIUM ION × 2 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID × 2 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1jvs 1k5h 1k5h 1onn 1ono 1onp 1q0h 1q0l 1q0q 1t1r 1t1s 2egh

16 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name DXR_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 12–408； UniProt 2–398 Author chain B； PDBConstruct 12–408； UniProt 2–398

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id2egh
Deposition date deposition_date2007-03-01
Structure title titleCrystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with a magnesium ion, NADPH and fosmidomycin
Keywords keywordsProtein-inhibitor complex, Oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2egh__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2egh__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2egh__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）30.91 Å
Rg (electron density)30.29 Å
Total Rg31.00 Å
Atom count6181
Residues798
Excluded volume109750 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2egh__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd2egha1
Class classa — All alpha proteins
Fold Fold folda.69 — Left-handed superhelix
Superfamily Superfamily superfamilya.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Family Family familya.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Domain ID domain_idd2egha2
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_idd2egha3
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
Domain ID domain_idd2egha4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2egha5
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2eghb1
Class classa — All alpha proteins
Fold Fold folda.69 — Left-handed superhelix
Superfamily Superfamily superfamilya.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Family Family familya.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Domain ID domain_idd2eghb2
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_idd2eghb3
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
Domain ID domain_idd2eghb4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id2eghA01
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_id2eghA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily10 — RNA polymerase sigma factor, region 2, helix turn helix motif
Domain ID domain_id2eghB01
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_id2eghB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily10 — RNA polymerase sigma factor, region 2, helix turn helix motif
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7. Citations (1)