6ldh

REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

M4 APO-LACTATE DEHYDROGENASE

Squalus acanthias

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDHA_SQUAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–330； UniProt 1–329

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_id	6ldh
Deposition date deposition_date	1987-11-25
Structure title title	REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE
Keywords keywords	OXIDOREDUCTASE(CHOH(D)-NAD(A)); OXIDOREDUCTASE(CHOH(D)-NAD(A))
Experimental Method method	X-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.

6ldh__assembly_1__model_1

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

Download this curve (.dat)

6ldh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ldh__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.15 Å
Rg (electron density)	31.36 Å
Total Rg	31.96 Å
Atom count	10220
Residues	1316
Excluded volume	183880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ldh__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 (3)

Entity 1 Entity 1 polymer

Description description	M4 APO-LACTATE DEHYDROGENASE
Molecular weight formula_weight	36353.3 kDa
EC 编号 ec_number	1.1.1.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2841

XATLKDKLIGHLATSQEPRSYNKITVVGVGAVGMACAISILMKDLADEVALVDVMEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKHSPDCIILVVSNPVDVLTYVAWKLSGLPMHRIIGSGCNLDSARFRYLMGERLGVHSCSCHGWVIGEHGDSVPSVWSGMNVASIKLHPLDGTNKDKQDWKKLHKDVVDSAYEVIKLKGYTSWAIGLSVADLAETIMKNLCRVHPVSTMVKDFYGIKDNVFLSLPCVLNDHGISNIVKMKLKPNEEQQLQKSATTLWDIQKDLKF

Source Source

Source organism organism	Squalus acanthias
Common name common_name	spiny dogfish
NCBI taxonomy ID ncbi_taxonomy_id	7797

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	286

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6ldha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.5 — LDH N-terminal domain-like

Domain ID domain_id	d6ldha2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	6ldhA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	6ldhA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

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7. Citations (20)

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.

J.Mol.Biol. (1987)

PMID: 3430615 · DOI: 10.1016/0022-2836(87)90293-2 PRIMARY

Structural Adaptations of Lactate Dehydrogenase Isozymes

Proc.Natl.Acad.Sci.USA (1977)

A Comparison of the Structures of Apo Dogfish M4 Lactate Dehydrogenase and its Ternary Complexes

J.Mol.Biol. (1976)

A 5 Angstroms X-Ray Diffraction Study of Coenzyme-Deficient Lactate Dehydrogenase,Nad-Pyruvate Ternary Complex

J.Mol.Biol. (1975)

A Structural Comparison of Porcine B4 and Dogfish A4 Isozymes of Lactate Dehydrogenase

Isozymes-Molecular Structure (1975)

Lactate Dehydrogenase

The Enzymes,Third Edition (1975)

X-Ray Studies of Protein Interactions

Annu.Rev.Biochem. (1974)

Chemical and Biological Evolution of a Nucleotide Binding Protein

Nature (1974)

Recognition of Structural Domains in Globular Proteins

J.Mol.Biol. (1974)

Structure-Function Relationships in Lactate Dehydrogenase

Proc.Natl.Acad.Sci.USA (1973)

Amino-Acid Sequence of Dogfish M4 Lactate Dehydrogenase

Proc.Natl.Acad.Sci.USA (1973)

Molecular Symmetry Axes and Subunit Interfaces in Certain Dehydrogenases

J.Mol.Biol. (1973)

Functional Anion Binding Sites in Dogfish M4 Lactate Dehydrogenase

J.Mol.Biol. (1973)

Binding of Oxamate to the Apoenzyme of Dogfish M4 Lactate Dehydrogenase

J.Mol.Biol. (1973)

Conformation of Coenzyme Fragments When Bound to Lactate Dehydrogenase

J.Mol.Biol. (1973)

Atomic Co-Ordinates for Dogfish M4 Apo-Lactate Dehydrogenase

Biochem.Biophys.Res.Commun. (1973)

The 5 Angstroms Resolution Structure of an Abortive Ternary Complex of Lactate Dehydrogenase and its Comparison with the Apo-Enzyme

J.Mol.Biol. (1971)

Structure of Lactate Dehydrogenase at 2.8 Angstroms Resolution

Nature (1970)

Low Resolution Study of Crystalline L-Lactate Dehydrogenase

J.Mol.Biol. (1969)

The Crystal Structure of Lactic Dehydrogenase

Proc.Natl.Acad.Sci.USA (1967)

Unit-cell length a length_a	146.800 Å
Unit-cell length b length_b	146.800 Å
Unit-cell length c length_c	155.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	F 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2020
R_work r_work	—
R_free r_free	—

REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

M4 APO-LACTATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ldh__assembly_1__model_1

6ldh__assembly_1__model_1 | I(q)

6ldh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (20)

REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

M4 APO-LACTATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ldh__assembly_1__model_1

6ldh__assembly_1__model_1 | I(q)

6ldh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (20)