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6ka0

Silver-bound 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 K-12

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 SILVER ION × 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 1 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 SILVER ION × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 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_id6ka0
Deposition date deposition_date2019-06-19
Structure title titleSilver-bound E.coli Malate dehydrogenase
Keywords keywordssilver nano-particle, dehydrogenase, glyoxylate cycle, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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.

6ka0__assembly_2__model_1

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

Download this curve (.dat)

6ka0__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.

6ka0__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）26.39 Å
Rg (electron density)25.47 Å
Total Rg26.22 Å
Atom count4354
Residues600
Excluded volume78628 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6ka0__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6ka0__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) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6ka0A01
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_id6ka0A02
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_id6ka0B01
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_id6ka0B02
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_id6ka0C01
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_id6ka0C02
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_id6ka0D01
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_id6ka0D02
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 (1)