1zy8

The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.

Method: X-RAY DIFFRACTION

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

Dihydrolipoyl dehydrogenase, mitochondrial

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, mitochondrial × 1 （O00330） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component, mitochondrial × 1 （O00330） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component, mitochondrial × 1 （O00330） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component, mitochondrial × 1 （O00330） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase protein X component, mitochondrial × 1 （O00330） 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, mitochondrial

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, mitochondrial × 2 （P09622） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase, mitochondrial × 2 （P09622） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase, mitochondrial × 2 （P09622） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase, mitochondrial × 2 （P09622） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase, mitochondrial × 2 （P09622） 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 1–221； UniProt 54–274 Author chain L； PDBConstruct 1–221； UniProt 54–274 Author chain M； PDBConstruct 1–221； UniProt 54–274 Author chain N； PDBConstruct 1–221； UniProt 54–274 Author chain O； PDBConstruct 1–221； UniProt 54–274

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	1zy8
Deposition date deposition_date	2005-06-09
Structure title title	The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.
Keywords keywords	;human, dihydrolipoamide dehydrogenase, E3, dihydrolipoyl dehydrogenase, dihydrolipoamide dehydrogenase binding protein, E3-binding protein, pyruvate dehydrogenase complex, alpha-keto acid complex, flavin adenine dinucleotide cofactor, 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.

1zy8__assembly_1__model_1

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

Download this curve (.dat)

1zy8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zy8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.60 Å
Rg (electron density)	30.00 Å
Total Rg	30.70 Å
Atom count	7477
Residues	992
Excluded volume	133410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zy8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`1zy8__assembly_1__model_2`	trimeric （3）	Excluded	—	—
	Exclusion reason： The polymer contains overlapping alternate coordinates, and a complete, coherent single conformation cannot be selected automatically.
2	1	`1zy8__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`1zy8__assembly_2__model_2`	trimeric （3）	Excluded	—	—
	Exclusion reason： The polymer contains overlapping alternate coordinates, and a complete, coherent single conformation cannot be selected automatically.
3	1	`1zy8__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	2	`1zy8__assembly_3__model_2`	trimeric （3）	Excluded	—	—
	Exclusion reason： The polymer contains overlapping alternate coordinates, and a complete, coherent single conformation cannot be selected automatically.
4	1	`1zy8__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	2	`1zy8__assembly_4__model_2`	trimeric （3）	Excluded	—	—
	Exclusion reason： The polymer contains overlapping alternate coordinates, and a complete, coherent single conformation cannot be selected automatically.
5	1	`1zy8__assembly_5__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	2	`1zy8__assembly_5__model_2`	trimeric （3）	Excluded	—	—
	Exclusion reason： A polymer chain declared by the official assembly is absent from the generated coordinate model, leaving the structure composition incomplete.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Dihydrolipoyl dehydrogenase, mitochondrial
Molecular weight formula_weight	50236.5 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	75406

ADQPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCIPSKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGGIAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEVTPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDGKIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRIPVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAHPTLSEAFREANLAASFGKSINF

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, mitochondrial
Molecular weight formula_weight	24449.8 kDa
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

GDPIKILMPSLSPTMEEGNIVKWLKKEGEAVSAGDALCEIETDKAVVTLDASDDGILAKIVVEEGSKNIRLGSLIGLIVEEGEDWKHVEIPKDVGPPPPVSKPSEPRPSPEPQISIPVKKEHIPGTLRFRLSPAARNILEKHSLDASQGTATGPRGIFTKEDALKLVQLKQTGKITESRPTPAPTATPTAPSPLQATSGPSYPRPVIPPVSTPGQPNAVGTLEHHHHHH

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	492

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6. Fold Classification (SCOP + CATH) 35 domains

CATH v4.4 (35 domains)

Domain ID domain_id	1zy8A01
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	1zy8A02
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	1zy8A03
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	1zy8B01
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	1zy8B02
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	1zy8B03
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	1zy8C01
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	1zy8C02
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	1zy8C03
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	1zy8D01
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	1zy8D02
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	1zy8D03
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	1zy8E01
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	1zy8E02
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	1zy8E03
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	1zy8F01
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	1zy8F02
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	1zy8F03
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	1zy8G01
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	1zy8G02
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	1zy8G03
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	1zy8H01
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	1zy8H02
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	1zy8H03
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	1zy8I01
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	1zy8I02
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	1zy8I03
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	1zy8J01
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	1zy8J02
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	1zy8J03
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	1zy8K00
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	1zy8L00
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	1zy8M00
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	1zy8N00
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	1zy8O00
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	168.790 Å
Unit-cell length b length_b	186.910 Å
Unit-cell length c length_c	217.540 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	2.590 Å
Low-resolution limit resolution_low	45.640 Å
R factor r_factor	0.2750
R_work r_work	0.2080
R_free r_free	0.2759

The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.

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

Dihydrolipoyl dehydrogenase, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Pyruvate dehydrogenase protein X component, mitochondrial

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

1zy8__assembly_1__model_1

1zy8__assembly_1__model_1 | I(q)

1zy8__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 35 domains

CATH v4.4 (35 domains)

7. Citations (1)

The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.

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

Dihydrolipoyl dehydrogenase, mitochondrial

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, mitochondrial

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

1zy8__assembly_1__model_1

1zy8__assembly_1__model_1 | I(q)

1zy8__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 35 domains

CATH v4.4 (35 domains)

7. Citations (1)