SAXSdb — 7dbj

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

L-lactate dehydrogenase B chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 OXAMIC ACID × 4 1,2-ETHANEDIOL × 7 N-[[3-[2-[(phenylmethyl)amino]ethyl]-1H-indol-2-yl]methyl]cycloheptanamine × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDHB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–333； UniProt 2–334 Author chain B； PDBConstruct 1–333； UniProt 2–334 Author chain C； PDBConstruct 1–333； UniProt 2–334 Author chain D； PDBConstruct 1–333； UniProt 2–334

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	7dbj
Deposition date deposition_date	2020-10-20
Structure title title	Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046
Keywords keywords	Lactate dehydrogenase, Inhibitor, Complex, OXIDOREDUCTASE; 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.

7dbj__assembly_1__model_1

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

Download this curve (.dat)

7dbj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7dbj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.12 Å
Rg (electron density)	31.04 Å
Total Rg	31.72 Å
Atom count	10528
Residues	1332
Excluded volume	189340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7dbj__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 (6)

Entity 1 Entity 1 polymer

Description description	L-lactate dehydrogenase B chain
Molecular weight formula_weight	36548.2 kDa
EC 编号 ec_number	1.1.1.27
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11302

ATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	OXAMIC ACID
Molecular weight formula_weight	89.0 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	N-[[3-[2-[(phenylmethyl)amino]ethyl]-1H-indol-2-yl]methyl]cycloheptanamine
Molecular weight formula_weight	375.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	765

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	7dbjA01
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	7dbjA02
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	7dbjB01
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	7dbjB02
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	7dbjC01
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	7dbjC02
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	7dbjD01
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	7dbjD02
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	59.389 Å
Unit-cell length b length_b	137.577 Å
Unit-cell length c length_c	84.909 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.551 Å
Low-resolution limit resolution_low	43.496 Å
R factor r_factor	—
R_work r_work	0.1697
R_free r_free	0.1917

Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046

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

L-lactate dehydrogenase B 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

7dbj__assembly_1__model_1

7dbj__assembly_1__model_1 | I(q)

7dbj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046

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

L-lactate dehydrogenase B 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

7dbj__assembly_1__model_1

7dbj__assembly_1__model_1 | I(q)

7dbj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)