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Crystal structure of the pce reductive dehalogenase from S. multivorans P2(1) crystal form
Analyse Crystal structure of the pce reductive dehalogenase from S. multivorans P2(1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UR3
- Type
- protein
- Length
- 2,637 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrachloroethene reductive dehalogenase catalytic subunit
- EC
- 1.97.1.8
- UniProt
- W6EQP0
- Ligands
- SF4, BVQ
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrachloroethene reductive dehalogenase catalytic subunit (EC 1.97.1.8) | protein | 458 | 40% helix, 17% strand | W6EQP0 |
| B | Tetrachloroethene reductive dehalogenase catalytic subunit (EC 1.97.1.8) | protein | 436 | 37% helix, 17% strand | W6EQP0 |
| C | Tetrachloroethene reductive dehalogenase catalytic subunit (EC 1.97.1.8) | protein | 442 | 39% helix, 17% strand | W6EQP0 |
| D | Tetrachloroethene reductive dehalogenase catalytic subunit (EC 1.97.1.8) | protein | 437 | 37% helix, 17% strand | W6EQP0 |
| E | Tetrachloroethene reductive dehalogenase catalytic subunit (EC 1.97.1.8) | protein | 435 | 36% helix, 16% strand | W6EQP0 |
| F | Tetrachloroethene reductive dehalogenase catalytic subunit (EC 1.97.1.8) | protein | 429 | 35% helix, 17% strand | W6EQP0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains A, B, C, D, E, F
- BVQ · Norpseudo-B12 · ligand · 6 copies · chains A, B, C, D, E, F
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.88 | 0.89 | 85 | SF4, BVQ |
| 2 | 1079 | 0.88 | 0.88 | 85 | SF4, BVQ |
| 3 | 1081 | 0.87 | 0.88 | 84 | SF4, BVQ |
| 4 | 1130 | 0.87 | 0.88 | 90 | SF4, BVQ |
| 5 | 1120 | 0.87 | 0.87 | 88 | SF4, BVQ |
Interfaces
7 interfaces between chains.
- E–F · 4198 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 4174 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 4165 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 614 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 160 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4UR3 · Crystal structure of the PCE reductive dehalogenase from S. multivorans P2(1) crystal form · 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 4UR3 · PDBe 4UR3 · UniProt W6EQP0
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