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1ib6

CRYSTAL STRUCTURE OF R153C E. COLI MALATE DEHYDROGENASE

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

MALATE DEHYDROGENASE

Escherichia coli

UniProt P61889

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 SULFATE ION × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 SULFATE ION × 4 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5z3w 5z3w 5z3w 5z3w 7cgc 7cgc 7cgc 7cgc 7cgd 7cgd 7cgd 7cgd

16 assemblies; showing the first 12

Homodimer
1emd 1ib6 1ib6 1ie3 1ie3 2cmd 2pwz 2pwz 3hhp 3hhp 5kka 6ka0

15 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name MDH_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–312； UniProt 1–312 Author chain B； PDBConstruct 1–312； UniProt 1–312 Author chain C； PDBConstruct 1–312； UniProt 1–312 Author chain D； PDBConstruct 1–312； UniProt 1–312

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_id1ib6
Deposition date deposition_date2001-03-27
Structure title titleCRYSTAL STRUCTURE OF R153C E. COLI MALATE DEHYDROGENASE
Keywords keywordsOXIDOREDUCTASE, DEHYDROGENASE, MALATE DEHYDROGENASE, SUBSTRATE SPECIFICITY; 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.

1ib6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ib6__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1ib6__assembly_2__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）26.47 Å
Rg (electron density)25.64 Å
Total Rg26.37 Å
Atom count4642
Residues624
Excluded volume83245 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ib6__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1ib6__assembly_2__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 (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1ib6a1
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.2.1.5 — LDH N-terminal domain-like
Domain ID domain_idd1ib6a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamilyd.162.1 — LDH C-terminal domain-like
Family Family familyd.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain
Domain ID domain_idd1ib6b1
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.2.1.5 — LDH N-terminal domain-like
Domain ID domain_idd1ib6b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamilyd.162.1 — LDH C-terminal domain-like
Family Family familyd.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain
Domain ID domain_idd1ib6c1
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.2.1.5 — LDH N-terminal domain-like
Domain ID domain_idd1ib6c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamilyd.162.1 — LDH C-terminal domain-like
Family Family familyd.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain
Domain ID domain_idd1ib6d1
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.2.1.5 — LDH N-terminal domain-like
Domain ID domain_idd1ib6d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamilyd.162.1 — LDH C-terminal domain-like
Family Family familyd.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id1ib6A01
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_id1ib6A02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
Domain ID domain_id1ib6B01
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_id1ib6B02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
Domain ID domain_id1ib6C01
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_id1ib6C02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
Domain ID domain_id1ib6D01
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_id1ib6D02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
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7. Citations (2)