Research workbench
Putative oxidoreductase from escherichia COLI str. K-12
Analyse Putative oxidoreductase from escherichia COLI str. K-12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OZ7
- Type
- protein
- Length
- 1,912 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized oxidoreductase yohf
- EC
- 1.-.-.-
- UniProt
- P33368
- Ligands
- CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized oxidoreductase yohf (EC 1.-.-.-) | protein | 242 | 46% helix, 17% strand | P33368 |
| B | Uncharacterized oxidoreductase yohf (EC 1.-.-.-) | protein | 236 | 46% helix, 18% strand | P33368 |
| C, G | Uncharacterized oxidoreductase yohf (EC 1.-.-.-) | protein | 241 | 44% helix, 17% strand | P33368 |
| D | Uncharacterized oxidoreductase yohf (EC 1.-.-.-) | protein | 237 | 45% helix, 19% strand | P33368 |
| E | Uncharacterized oxidoreductase yohf (EC 1.-.-.-) | protein | 241 | 45% helix, 17% strand | P33368 |
| F | Uncharacterized oxidoreductase yohf (EC 1.-.-.-) | protein | 237 | 46% helix, 18% strand | P33368 |
| H | Uncharacterized oxidoreductase yohf (EC 1.-.-.-) | protein | 237 | 46% helix, 18% strand | P33368 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, G, E, F, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains E, G, F, H
- PGE · Triethylene glycol · additive · 2 copies · chains C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.84 | 0.85 | 72 | empty |
| 2 | 339 | 0.68 | 0.82 | 47 | empty |
| 3 | 320 | 0.65 | 0.80 | 45 | empty |
| 4 | 109 | 0.60 | 0.86 | 28 | empty |
| 5 | 360 | 0.58 | 0.75 | 35 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1770 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1761 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1758 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1749 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1694 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6OZ7 · Putative oxidoreductase from Escherichia coli str. K-12 · the same entry in another collection · chain H against H, TM-score 1.00
- P33368 · AlphaFold monomer V2.0 prediction for uncharacterized oxidoreductase yohf (P33368) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P33368
- Elsewhere: RCSB PDB 6OZ7 · PDBe 6OZ7 · UniProt P33368
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