MolNFT v1 · #142459 · protein

Structure of benzoylformate decarboxylases in complex with cofactor tpp

6A50: “Structure of benzoylformate decarboxylases in complex with cofactor tpp”. X-ray diffraction, 2 ligands (TPP, MG), 7 pockets (best druggability 0.79). MolNFT v1 #142459 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6A50
Type: protein
Length: 1,054 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Benzoylformate decarboxylases
EC: 4.1.1.7
Ligands: TPP, MG
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Benzoylformate decarboxylases (EC 4.1.1.7)	protein	527	39% helix, 18% strand	—

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	416	0.79	0.88	58	MG, TPP
2	533	0.79	0.85	71	MG, TPP
3	236	0.57	0.79	42	empty
4	132	0.56	0.83	35	empty
5	206	0.54	0.78	33	empty

Interfaces

1 interface between chains.

A–B · 3627 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

6A50 · structure of benzoylformate decarboxylases in complex with cofactor TPP · 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
Elsewhere: RCSB PDB 6A50 · PDBe 6A50

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