2f5z

Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein

Method: X-RAY DIFFRACTION

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

Dihydrolipoyl dehydrogenase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component × 1 （O00330） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component × 1 （O00330） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component × 1 （O00330） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component × 1 （O00330） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component × 1 （O00330） SULFATE ION × 7 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DLDH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–474； UniProt 36–509 Author chain B； PDBConstruct 1–474； UniProt 36–509 Author chain C； PDBConstruct 1–474； UniProt 36–509 Author chain D； PDBConstruct 1–474； UniProt 36–509 Author chain E； PDBConstruct 1–474； UniProt 36–509 Author chain F； PDBConstruct 1–474； UniProt 36–509 Author chain G； PDBConstruct 1–474； UniProt 36–509 Author chain H； PDBConstruct 1–474； UniProt 36–509 Author chain I； PDBConstruct 1–474； UniProt 36–509 Author chain J； PDBConstruct 1–474； UniProt 36–509

Pyruvate dehydrogenase protein X component

Homo sapiens

UniProt O00330

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase × 2 （P09622） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase × 2 （P09622） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase × 2 （P09622） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase × 2 （P09622） SULFATE ION × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase × 2 （P09622） SULFATE ION × 7 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODPX_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain K； PDBConstruct 1–58； UniProt 173–230 Author chain L； PDBConstruct 1–58； UniProt 173–230 Author chain M； PDBConstruct 1–58； UniProt 173–230 Author chain N； PDBConstruct 1–58； UniProt 173–230 Author chain O； PDBConstruct 1–58； UniProt 173–230

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	2f5z
Deposition date deposition_date	2005-11-28
Structure title title	Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein
Keywords keywords	protein-protein complex, OXIDOREDUCTASE-PROTEIN BINDING COMPLEX; OXIDOREDUCTASE/PROTEIN BINDING
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.

2f5z__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2f5z__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f5z__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	30.34 Å
Rg (electron density)	29.73 Å
Total Rg	30.44 Å
Atom count	7442
Residues	986
Excluded volume	132440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f5z__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2f5z__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2f5z__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2f5z__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2f5z__assembly_5__model_1`	trimeric （3）	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	Dihydrolipoyl dehydrogenase
Molecular weight formula_weight	50208.4 kDa
EC 编号 ec_number	1.8.1.4
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	40176

ADQPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCIPSKALLNNSHYYHMAHGTDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGGIAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEVTPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDGKIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRIPVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAHPTLSEAFREANLAASFGKSINF

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 protein X component
Molecular weight formula_weight	7150.2 kDa
Mutation mutation	K120G,T176L
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,L,M,N,O

GEHIPGTLRFRLSPAARNILEKHSLDASQGTATGPRGIFTKEDALKLVQLKQTGKILEHHHHHH

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

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	39

Entity 4 Entity 4 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1776

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6. Fold Classification (SCOP + CATH) 35 domains

CATH v4.4 (35 domains)

Domain ID domain_id	2f5zA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zC01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zC02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zD01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zD02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zE01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zE02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zE03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zF01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zF02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zF03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zG01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zG02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zG03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zH01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zH02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zH03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zI01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zI02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zI03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zJ01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zJ02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2f5zJ03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2f5zK00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	2f5zL00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	2f5zM00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	2f5zN00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	2f5zO00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

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Unit-cell length a length_a	171.153 Å
Unit-cell length b length_b	187.728 Å
Unit-cell length c length_c	224.392 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	40

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

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	37.400 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2420

Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein

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

Dihydrolipoyl dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Pyruvate dehydrogenase protein X component

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

2f5z__assembly_3__model_1

2f5z__assembly_3__model_1 | I(q)

2f5z__assembly_3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 35 domains

CATH v4.4 (35 domains)

7. Citations (1)

Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein

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

Dihydrolipoyl 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

Pyruvate dehydrogenase protein X component

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

2f5z__assembly_3__model_1

2f5z__assembly_3__model_1 | I(q)

2f5z__assembly_3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 35 domains

CATH v4.4 (35 domains)

7. Citations (1)