8s88

Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine

Method: X-RAY DIFFRACTION

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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	(3S)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine × 2 OXAMIC ACID × 4 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SULFATE ION × 4 GLYCEROL × 8 DI(HYDROXYETHYL)ETHER × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	(3S)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine × 3 OXAMIC ACID × 4 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SULFATE ION × 4 GLYCEROL × 5 DI(HYDROXYETHYL)ETHER × 2 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	OXAMIC ACID × 4 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SULFATE ION × 4 GLYCEROL × 6 DI(HYDROXYETHYL)ETHER × 3 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 1–334； UniProt 1–334 Author chain B； PDBConstruct 1–334； UniProt 1–334 Author chain C； PDBConstruct 1–334； UniProt 1–334 Author chain D； PDBConstruct 1–334； UniProt 1–334 Author chain E； PDBConstruct 1–334； UniProt 1–334 Author chain F； PDBConstruct 1–334； UniProt 1–334 Author chain G； PDBConstruct 1–334； UniProt 1–334 Author chain H； PDBConstruct 1–334； UniProt 1–334 Author chain I； PDBConstruct 1–334； UniProt 1–334 Author chain J； PDBConstruct 1–334； UniProt 1–334 Author chain K； PDBConstruct 1–334； UniProt 1–334 Author chain L； PDBConstruct 1–334； UniProt 1–334

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	8s88
Deposition date deposition_date	2024-03-06
Last revision last_revision	2025-03-19
Structure title title	Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine
Keywords keywords	Complex, Fluoxetine, 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.

8s88__assembly_1__model_1

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

Download this curve (.dat)

8s88__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8s88__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.10 Å
Rg (electron density)	31.05 Å
Total Rg	31.73 Å
Atom count	10719
Residues	1333
Excluded volume	190530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8s88__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8s88__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8s88__assembly_3__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 (9)

Entity 1 Entity 1 polymer

Description description	L-lactate dehydrogenase B chain
Molecular weight formula_weight	38602.4 kDa
EC 编号 ec_number	1.1.1.27
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	33474

MATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDLENLYFQGLEHHHHHH

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(3S)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine
Molecular weight formula_weight	309.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	OXAMIC ACID
Molecular weight formula_weight	89.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 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	12

Entity 5 Entity 5 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 8 Entity 8 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1337

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Unit-cell length a length_a	66.530 Å
Unit-cell length b length_b	413.960 Å
Unit-cell length c length_c	85.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.070 Å
Low-resolution limit resolution_low	48.670 Å
R factor r_factor	0.2156
R_work r_work	0.2129
R_free r_free	0.2638

Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine

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

8s88__assembly_1__model_1

8s88__assembly_1__model_1 | I(q)

8s88__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 (9)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine

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

8s88__assembly_1__model_1

8s88__assembly_1__model_1 | I(q)

8s88__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 (9)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)