1ni4

HUMAN PYRUVATE DEHYDROGENASE

Method: X-RAY DIFFRACTION

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

Pyruvate dehydrogenase E1 component: Alpha subunit

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Pyruvate dehydrogenase E1 component: Beta subunit × 2 （P11177） MAGNESIUM ION × 2 THIAMINE DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODPA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–365； UniProt 30–390 Author chain C； PDBConstruct 5–365； UniProt 30–390

Pyruvate dehydrogenase E1 component: Beta subunit

Homo sapiens

UniProt P11177

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Pyruvate dehydrogenase E1 component: Alpha subunit × 2 （P08559） MAGNESIUM ION × 2 THIAMINE DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODPB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 13–341； UniProt 32–359 Author chain D； PDBConstruct 13–341； UniProt 32–359

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	1ni4
Deposition date deposition_date	2002-12-20
Structure title title	HUMAN PYRUVATE DEHYDROGENASE
Keywords keywords	THIAMIN PYROPHOSPHATE, PYRUVATE, ALPHA-KETO ACID DEHYDROGENASE, PYRUVATE DEHYDROGENASE, 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.

1ni4__assembly_1__model_1

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

Download this curve (.dat)

1ni4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ni4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.57 Å
Rg (electron density)	31.87 Å
Total Rg	32.42 Å
Atom count	10754
Residues	1334
Excluded volume	192180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ni4__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	Pyruvate dehydrogenase E1 component: Alpha subunit
Molecular weight formula_weight	41277.2 kDa
EC 编号 ec_number	1.2.4.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	11496

MRGSFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRKGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGPILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFATADPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSVS

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 polymer

Description description	Pyruvate dehydrogenase E1 component: Beta subunit
Molecular weight formula_weight	37956.5 kDa
EC 编号 ec_number	1.2.4.1
Mutation mutation	V31L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MRGSHHHHHHGSLQVTVRDAINQGMDEELERDEKVFLLGEEVAQYDGAYKVSRGLWKKYGDKRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQPVPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVPFEFPPEAQSKDFLIPIGKAKIERQGTHITVVSHSRPVGHCLEAAAVLSKEGVECEVINMRTIRPMDMETIEASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSIPQVKDIIFAIKKTLNI

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 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 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	742

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1ni4a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d1ni4a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ni4b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

Domain ID domain_id	d1ni4b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

Domain ID domain_id	d1ni4b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ni4c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d1ni4c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ni4d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

Domain ID domain_id	d1ni4d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

Domain ID domain_id	d1ni4d3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	1ni4A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	1ni4B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	1ni4B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	1ni4C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	1ni4D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	1ni4D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

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Unit-cell length a length_a	64.337 Å
Unit-cell length b length_b	126.889 Å
Unit-cell length c length_c	190.638 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	45.170 Å
R factor r_factor	0.2020
R_work r_work	0.2020
R_free r_free	0.2440

HUMAN PYRUVATE DEHYDROGENASE

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

Pyruvate dehydrogenase E1 component: Alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Pyruvate dehydrogenase E1 component: Beta subunit

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

1ni4__assembly_1__model_1

1ni4__assembly_1__model_1 | I(q)

1ni4__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 polymer

Polymer Polymer

Source Source

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) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (2)

HUMAN PYRUVATE DEHYDROGENASE

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

Pyruvate dehydrogenase E1 component: Alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pyruvate dehydrogenase E1 component: Beta subunit

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

1ni4__assembly_1__model_1

1ni4__assembly_1__model_1 | I(q)

1ni4__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 polymer

Polymer Polymer

Source Source

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) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (2)