Research workbench
Crystal structure of the COG4313 outer membrane channel from Pseudomonas putida F1
Analyse Crystal structure of the COG4313 outer membrane channel from Pseudomonas putida… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RL8
- Type
- protein
- Length
- 1,070 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Pseudomonas putida
- Molecule
- Protein involved in meta-pathway of phenol degradation-like protein
- UniProt
- A5W3Z9
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 1% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein involved in meta-pathway of phenol degradation-like protein | protein | 267 | 1% helix, 67% strand | A5W3Z9 |
| C, D | Protein involved in meta-pathway of phenol degradation-like protein | protein | 268 | 1% helix, 67% strand | A5W3Z9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 28 copies · chains A, D, C, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.84 | 0.85 | 96 | C8E |
| 2 | 878 | 0.82 | 0.85 | 92 | C8E |
| 3 | 923 | 0.82 | 0.84 | 94 | C8E |
| 4 | 852 | 0.82 | 0.85 | 97 | C8E |
| 5 | 663 | 0.75 | 0.80 | 54 | C8E |
Interfaces
5 interfaces between chains.
- A–C · 733 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 716 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 231 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 216 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 210 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RL8 · Crystal structure of the COG4313 outer membrane channel from pseudomonas putida F1 · 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 A5W3Z9
- Elsewhere: RCSB PDB 4RL8 · PDBe 4RL8 · UniProt A5W3Z9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.