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Pce reductive dehalogenase from S. multivorans in complex with 2,4- dibromophenol

Analyse Pce reductive dehalogenase from S. multivorans in complex with 2,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M92
Type: protein
Length: 862 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tetrachloroethene reductive dehalogenase catalytic subunit pcea
UniProt: W6EQP0
Ligands: SF4, Y8I, BEN, BVQ, BR
Pockets: 7 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tetrachloroethene reductive dehalogenase catalytic subunit pcea	protein	443	37% helix, 17% strand	W6EQP0
B	Tetrachloroethene reductive dehalogenase catalytic subunit pcea	protein	419	38% helix, 16% strand	W6EQP0

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
Y8I · 2,4-bis(bromanyl)phenol · ligand · 4 copies · chains A, B
BEN · Benzamidine · ligand · 3 copies · chains A, B
BVQ · Norpseudo-B12 · ligand · 2 copies · chains A, B
BR · Bromide ion · ion · chains A
GOL · Glycerol · additive · 7 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	1134	0.88	0.88	101	SF4, BVQ, GOL, BEN, Y8I
2	1126	0.87	0.88	96	SF4, BVQ, BEN, GOL, Y8I, BR
3	328	0.76	0.88	54	empty
4	221	0.71	0.87	29	empty
5	364	0.61	0.77	33	GOL

Interfaces

1 interface between chains.

A–B · 4130 Å² buried · 71 hydrogen bonds · protein-protein

Compared structures

5M92 · PCE reductive dehalogenase from S. multivorans in complex with 2,4-dibromophenol · 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 W6EQP0
Elsewhere: RCSB PDB 5M92 · PDBe 5M92 · UniProt W6EQP0

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