SAXSdb — 2v65

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

L-LACTATE DEHYDROGENASE A CHAIN

CHAMPSOCEPHALUS GUNNARI

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDHA_CHAGU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–331； UniProt 1–330 Author chain B； PDBConstruct 2–331； UniProt 1–330

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	2v65
Deposition date deposition_date	2007-07-13
Structure title title	Apo LDH from the psychrophile C. gunnari
Keywords keywords	OXIDOREDUCTASE, LACTATE DEHYDROGENASE, NAD, FISH, GLYCOLYSIS; OXIDOREDUCTASE
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.

2v65__assembly_1__model_1

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

Download this curve (.dat)

2v65__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v65__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.94 Å
Rg (electron density)	30.91 Å
Total Rg	31.56 Å
Atom count	9952
Residues	1304
Excluded volume	179180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v65__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2v65__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2v65a1
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.2.1.0 — automated matches

Domain ID domain_id	d2v65a2
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.162.1.0 — automated matches

Domain ID domain_id	d2v65b1
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.2.1.0 — automated matches

Domain ID domain_id	d2v65b2
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.162.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2v65A01
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	2v65A02
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

Domain ID domain_id	2v65B01
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	2v65B02
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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Unit-cell length a length_a	113.790 Å
Unit-cell length b length_b	113.790 Å
Unit-cell length c length_c	109.900 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	16

Space group space_group	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	19.790 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2410

Description description	L-LACTATE DEHYDROGENASE A CHAIN
Molecular weight formula_weight	36202.9 kDa
EC 编号 ec_number	1.1.1.27
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5277

Apo LDH from the psychrophile C. gunnari

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

L-LACTATE DEHYDROGENASE A CHAIN

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

2v65__assembly_1__model_1

2v65__assembly_1__model_1 | I(q)

2v65__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	CHAMPSOCEPHALUS GUNNARI
Common name common_name	MACKEREL ICEFISH
NCBI taxonomy ID ncbi_taxonomy_id	52237
Host organism host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	305

Apo LDH from the psychrophile C. gunnari

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

L-LACTATE DEHYDROGENASE A CHAIN

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

2v65__assembly_1__model_1

2v65__assembly_1__model_1 | I(q)

2v65__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)