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Crystal structure of the pyruvate dehydrogenase (E1P) component of human pyruvate dehydrogenase complex

Analyse Crystal structure of the pyruvate dehydrogenase (E1P) component of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EXG
Type: protein
Length: 10,765 residues
Chains: 32
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial; Pyruvate…
EC: 1.2.4.1
UniProt: P08559, P11177
Ligands: K
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 12 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	342	44% helix, 15% strand	P08559
B, D, F, H, J, L, N, P, R, T, V, X, Z, 2, 4, 6	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (EC 1.2.4.1)	protein	329	41% helix, 17% strand	P11177
E, M, Y	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	349	44% helix, 15% strand	P08559
G	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	346	43% helix, 15% strand	P08559
I, Q	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	344	43% helix, 15% strand	P08559
K, 5	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	347	43% helix, 15% strand	P08559
O	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	332	42% helix, 15% strand	P08559
S	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	340	43% helix, 14% strand	P08559
U	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	348	44% helix, 16% strand	P08559
W	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	345	44% helix, 14% strand	P08559
1	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	335	39% helix, 15% strand	P08559
3	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1)	protein	342	43% helix, 15% strand	P08559

Ligands and binding sites

K · Potassium ion · metal · 16 copies · chains B, D, F, H, J, L, N, P, R, T, V, X, Z, 2, 4, 6

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	98	0.76	0.97	30	empty
2	95	0.76	0.97	30	empty
3	89	0.75	0.97	28	empty
4	942	0.75	0.78	104	empty
5	96	0.74	0.96	32	empty

Interfaces

67 interfaces between chains.

V–X · 2503 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 2495 Å² buried · 31 hydrogen bonds · protein-protein
J–L · 2494 Å² buried · 29 hydrogen bonds · protein-protein
4–6 · 2492 Å² buried · 30 hydrogen bonds · protein-protein
R–T · 2492 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

3EXG · Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate… · the same entry in another collection · chain B against B, 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 P08559
Every structure of UniProt P11177
Elsewhere: RCSB PDB 3EXG · PDBe 3EXG · UniProt P08559 · UniProt P11177

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