MolNFT v1 · #126639 · protein
Pce reductive dehalogenase from S. multivorans in complex with 4- bromophenol
5M8U · Tetrachloroethene reductive dehalogenase catalytically…: “Pce reductive dehalogenase from S. multivorans in complex with 4- bromophenol”. X-ray diffraction, 4 ligands (SF4, BML, BVQ), 8 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 5M8U
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrachloroethene reductive dehalogenase catalytically active subunit
- UniProt
- O68252
- Ligands
- SF4, BML, BVQ, 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 catalytically active subunit | protein | 444 | 38% helix, 17% strand | O68252 |
| B | Tetrachloroethene reductive dehalogenase catalytically active subunit | protein | 418 | 38% helix, 17% strand | O68252 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- BML · 4-bromophenol · ligand · 4 copies · chains A, B
- BVQ · Norpseudo-B12 · ligand · 2 copies · chains A, B
- BEN · Benzamidine · ligand · chains A
- GOL · Glycerol · additive · 8 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 | 1077 | 0.88 | 0.88 | 90 | SF4, BVQ, BEN, GOL, BML |
| 2 | 1136 | 0.87 | 0.88 | 103 | BML, SF4, BVQ, GOL |
| 3 | 222 | 0.71 | 0.87 | 27 | empty |
| 4 | 246 | 0.68 | 0.85 | 32 | empty |
| 5 | 55 | 0.65 | 0.95 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4127 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 5M8U · PCE reductive dehalogenase from S. multivorans in complex with 4-bromophenol · 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 O68252
- Elsewhere: RCSB PDB 5M8U · PDBe 5M8U · UniProt O68252
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