MolNFT v1 · #105972 · protein
Crystal structure of the COG4313 outer membrane channel from pseudomonas putida F1
4RL8 · Protein involved in meta-pathway of phenol degradation-like…: “Crystal structure of the COG4313 outer membrane channel from pseudomonas putida F1”. X-ray diffraction, 1 ligand (PO4), 10 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 4RL8
- Type
- protein
- Length
- 1,070 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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
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