MolNFT v1 · #129145 · protein
Pce reductive dehalogenase from S. multivorans with 6- hydroxybenzimidazolyl norcobamide cofactor
5OBP · Tetrachloroethene reductive dehalogenase catalytically…: “Pce reductive dehalogenase from S. multivorans with 6- hydroxybenzimidazolyl norcobamide cofactor”. X-ray diffraction, 3 ligands (SF4, 9QQ, BEN), 10 pockets (best…
- PDB
- 5OBP
- 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, 9QQ, BEN
- Pockets
- 10 · 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 catalytically active subunit | protein | 444 | 36% helix, 17% strand | O68252 |
| B | Tetrachloroethene reductive dehalogenase catalytically active subunit | protein | 418 | 39% helix, 17% strand | O68252 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- 9QQ · 6-hydroxybenzimidazolyl-norcobamide · ligand · 2 copies · chains A, B
- BEN · Benzamidine · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.88 | 0.88 | 87 | SF4, 9QQ |
| 2 | 1097 | 0.87 | 0.88 | 89 | SF4, 9QQ, BEN |
| 3 | 280 | 0.72 | 0.86 | 38 | empty |
| 4 | 66 | 0.70 | 0.96 | 26 | empty |
| 5 | 264 | 0.67 | 0.84 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 4117 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 5OBP · PCE reductive dehalogenase from S. multivorans with 6-hydroxybenzimidazolyl norcobamide… · 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 5OBP · PDBe 5OBP · UniProt O68252
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