MolNFT v1 · #14553 · protein

Benzoylformate decarboxylase from pseudomonas putida complexed with an inhibitor, R-mandelate

1MCZ: “Benzoylformate decarboxylase from pseudomonas putida complexed with an inhibitor, R-mandelate”. X-ray diffraction, 3 ligands (TPP, RMN, MG), 20 pockets (best druggability 0.91). MolNFT v1 #14553 on GenesisL1: 3D structure, binding…

PDB: 1MCZ
Type: protein
Length: 8,384 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Benzoylformate decarboxylase
EC: 4.1.1.7
UniProt: P20906
Ligands: TPP, RMN, MG
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	Benzoylformate decarboxylase (EC 4.1.1.7)	protein	524	39% helix, 19% strand	P20906

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
RMN · (R)-mandelic acid · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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	1023	0.91	0.93	155	empty
2	603	0.88	0.93	88	empty
3	468	0.86	0.93	78	empty
4	390	0.85	0.94	68	MG
5	384	0.85	0.93	63	empty

Interfaces

41 interfaces between chains.

C–D · 3618 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 3606 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 3602 Å² buried · 33 hydrogen bonds · protein-protein
K–L · 3600 Å² buried · 27 hydrogen bonds · protein-protein
I–J · 3598 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

1MCZ · Benzoylformate decarboxylase from pseudomonas putida complexed with an inhibitor… · the same entry in another collection · chain P against P, 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 P20906
Elsewhere: RCSB PDB 1MCZ · PDBe 1MCZ · UniProt P20906

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