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1d3a

CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM

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

HALOPHILIC MALATE DEHYDROGENASE

Haloarcula marismortui

UniProt Q07841

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 CHLORIDE ION × 4 SODIUM ION × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1hlp

1 assemblies

Homotetramer
1d3a 1o6z 2hlp 2j5k 2j5q 2j5r 2x0r 4jco 7q3x

9 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name MDH_HALMA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–303； UniProt 2–304 Author chain B； PDBConstruct 1–303； UniProt 2–304

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_id1d3a
Deposition date deposition_date1999-09-28
Structure title titleCRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
Keywords keywordsROSSMANN FOLD AND 3 SORTS OF COMPLEX SALT BRIDGES, 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.

1d3a__assembly_1__model_1

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

Download this curve (.dat)

1d3a__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.

1d3a__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）32.22 Å
Rg (electron density)31.02 Å
Total Rg31.68 Å
Atom count9210
Residues1212
Excluded volume160160 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1d3a__assembly_1__model_1 tetrameric （4） 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

SCOP 2.08 (4 domains)

Domain ID domain_idd1d3aa1
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_idd1d3aa2
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_idd1d3ab1
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_idd1d3ab2
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 (4 domains)

Domain ID domain_id1d3aA01
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_id1d3aA02
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_id1d3aB01
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_id1d3aB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
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7. Citations (5)