MolNFT v1 · #13335 · protein

E. COLI pyruvate dehydrogenase

1L8A · Pyruvate dehydrogenase E1 component: “E. COLI pyruvate dehydrogenase”. X-ray diffraction, 2 ligands (TPP, MG), 17 pockets (best druggability 0.71). MolNFT v1 #13335 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1L8A
Type: protein
Length: 1,602 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate dehydrogenase E1 component
EC: 1.2.4.1
UniProt: P06958
Ligands: TPP, MG
Pockets: 17 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyruvate dehydrogenase E1 component (EC 1.2.4.1)	protein	801	44% helix, 12% strand	P06958

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	408	0.71	0.82	51	TPP
2	388	0.70	0.82	61	MG, TPP
3	351	0.70	0.82	37	empty
4	215	0.69	0.86	26	empty
5	351	0.65	0.80	43	empty

Interfaces

1 interface between chains.

A–B · 5862 Å² buried · 116 hydrogen bonds · protein-protein

Compared structures

1L8A · E. COLI pyruvate dehydrogenase · the same entry in another collection · chain A against A, 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 P06958
Elsewhere: RCSB PDB 1L8A · PDBe 1L8A · UniProt P06958

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