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Crystal structure of the pce reductive dehalogenase from S. multivorans in complex with dibromoethene
Analyse Crystal structure of the pce reductive dehalogenase from S. multivorans in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UR1
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrachloroethene reductive dehalogenase catalytic subunit pcea
- EC
- 1.97.1.8
- UniProt
- W6EQP0
- Ligands
- SF4, BEN, BVQ, CB0
- Pockets
- 9 · 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 (EC 1.97.1.8) | protein | 449 | 37% helix, 17% strand | W6EQP0 |
| B | Tetrachloroethene reductive dehalogenase catalytic subunit pcea (EC 1.97.1.8) | protein | 438 | 36% helix, 17% strand | W6EQP0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- BEN · Benzamidine · ligand · 3 copies · chains A, B
- BVQ · Norpseudo-B12 · ligand · 2 copies · chains A, B
- CB0 · Cis-dibromoethene · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.88 | 0.89 | 78 | SF4, BVQ, CB0, GOL |
| 2 | 1105 | 0.87 | 0.88 | 95 | SF4, BVQ, CB0, BEN, GOL |
| 3 | 290 | 0.75 | 0.87 | 39 | empty |
| 4 | 265 | 0.69 | 0.84 | 34 | empty |
| 5 | 54 | 0.68 | 0.97 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4100 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 4UR1 · Crystal structure of the PCE reductive dehalogenase from S. multivorans in complex with… · 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 4UR1 · PDBe 4UR1 · UniProt W6EQP0
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