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

Analyse The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZY8
Type: protein
Length: 4,960 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrolipoyl dehydrogenase, mitochondrial; Pyruvate dehydrogenase protein X component…
EC: 1.8.1.4
UniProt: P09622, O00330
Ligands: FAD
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4)	protein	474	35% helix, 27% strand	P09622
K, L, M, N, O	Pyruvate dehydrogenase protein X component, mitochondrial	protein	44	50% helix, 5% strand	O00330

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	866	0.84	0.86	79	empty
2	656	0.84	0.88	60	empty
3	847	0.83	0.86	69	empty
4	826	0.83	0.86	67	empty
5	869	0.83	0.85	77	empty

Interfaces

26 interfaces between chains.

C–D · 3959 Å² buried · 64 hydrogen bonds · protein-protein
I–J · 3959 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 3938 Å² buried · 61 hydrogen bonds · protein-protein
G–H · 3861 Å² buried · 49 hydrogen bonds · protein-protein
E–F · 3857 Å² buried · 46 hydrogen bonds · protein-protein

Compared structures

1ZY8 · The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide… · the same entry in another collection · chain K against K, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P09622
Every structure of UniProt O00330
Elsewhere: RCSB PDB 1ZY8 · PDBe 1ZY8 · UniProt P09622 · UniProt O00330

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