2ldb

STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE

Method: X-RAY DIFFRACTION

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

L-LACTATE DEHYDROGENASE

Geobacillus stearothermophilus

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 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 1,6-di-O-phosphono-beta-D-fructofuranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDH_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317 Author chain C； PDBConstruct 1–317； UniProt 1–317 Author chain D； PDBConstruct 1–317； UniProt 1–317

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	2ldb
Deposition date deposition_date	1989-03-27
Structure title title	STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS 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.

2ldb__assembly_1__model_1

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

Download this curve (.dat)

2ldb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ldb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.36 Å
Rg (electron density)	30.41 Å
Total Rg	31.06 Å
Atom count	9600
Residues	1204
Excluded volume	170630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ldb__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 (5)

Entity 1 Entity 1 polymer

Description description	L-LACTATE DEHYDROGENASE
Molecular weight formula_weight	34902.7 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	9650

MKNNGGARVVVIGAGFVGASYVFALMNQGIADEIVLIDANESKAIGDAMDFNHGKVFAPKPVDIWHGDYDDCRDADLVVICAGANQKPGETRLDLVDKNIAIFRSIVESVMASGFQGLFLVATNPVDILTYATWKFSGLPHERVIGSGTILDTARFRFLLGEYFSVAPQNVHAYIIGEHGDTELPVWSQAYIGVMPIRKLVESKGEEAQKDLERIFVNVRDAAYQIIEKKGATYYGIAMGLARVTRAILHNENAILTVSAYLDGLYGERDVYIGVPAVINRNGIREVIEIELNDDEKNRFHHSAATLKSVLARAFTR

Source Source

Source organism organism	Geobacillus stearothermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1422

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	8

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,6-di-O-phosphono-beta-D-fructofuranose
Molecular weight formula_weight	340.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2ldba1
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	d2ldba2
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

Domain ID domain_id	d2ldbb1
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	d2ldbb2
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

Domain ID domain_id	d2ldbc1
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	d2ldbc2
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

Domain ID domain_id	d2ldbd1
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	d2ldbd2
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 (8 domains)

Domain ID domain_id	2ldbA01
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	2ldbA02
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	2ldbB01
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	2ldbB02
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	2ldbC01
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	2ldbC02
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	2ldbD01
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	2ldbD02
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	86.800 Å
Unit-cell length b length_b	86.800 Å
Unit-cell length c length_c	356.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2600
R_work r_work	—
R_free r_free	—

STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE

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

L-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

2ldb__assembly_1__model_1

2ldb__assembly_1__model_1 | I(q)

2ldb__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)

STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE

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

L-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

2ldb__assembly_1__model_1

2ldb__assembly_1__model_1 | I(q)

2ldb__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)