Research workbench
Pce reductive dehalogenase from S. multivorans in complex with 2,4,5- trichlorophenol
Analyse Pce reductive dehalogenase from S. multivorans in complex with 2,4,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M8X
- Type
- protein
- Length
- 869 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, BVQ, TC7, BEN
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrachloroethene reductive dehalogenase catalytic subunit pcea | protein | 449 | 37% helix, 17% strand | W6EQP0 |
| B | Tetrachloroethene reductive dehalogenase catalytic subunit pcea | protein | 420 | 39% helix, 16% strand | W6EQP0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- BVQ · Norpseudo-B12 · ligand · 2 copies · chains A, B
- TC7 · 2,4,5-trichlorophenol · ligand · 2 copies · chains A, B
- BEN · Benzamidine · ligand · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.88 | 0.88 | 91 | SF4, BVQ, BEN, GOL, TC7 |
| 2 | 1155 | 0.87 | 0.88 | 101 | SF4, BVQ, GOL, TC7 |
| 3 | 280 | 0.72 | 0.86 | 45 | empty |
| 4 | 243 | 0.70 | 0.86 | 33 | empty |
| 5 | 65 | 0.67 | 0.95 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 4125 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 5M8X · PCE reductive dehalogenase from S. multivorans in complex with 2,4,5-trichlorophenol · 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 5M8X · PDBe 5M8X · UniProt W6EQP0
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