Research workbench
An arginine ladder in oprp mediates phosphate specific transfer across the outer membrane
Analyse An arginine ladder in oprp mediates phosphate specific transfer across the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O4V
- Type
- protein
- Length
- 1,233 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porin P
- UniProt
- P05695
- Ligands
- CA, PO4, CL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Porin P | protein | 411 | 5% helix, 56% strand | P05695 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, C
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 | 957 | 0.82 | 0.83 | 94 | PO4 |
| 2 | 1189 | 0.80 | 0.82 | 113 | PO4, GOL |
| 3 | 1196 | 0.79 | 0.81 | 120 | PO4, GOL |
| 4 | 62 | 0.75 | 0.99 | 17 | CL |
| 5 | 221 | 0.56 | 0.78 | 28 | C8E |
Interfaces
3 interfaces between chains.
- A–B · 2076 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2067 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2060 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2O4V · An arginine ladder in OprP mediates phosphate specific transfer across the outer membrane · the same entry in another collection · chain B against B, TM-score 1.00
- P05695 · AlphaFold monomer V2.0 prediction for porin P (P05695) · a predicted model of the same protein · 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 P05695
- Elsewhere: RCSB PDB 2O4V · PDBe 2O4V · UniProt P05695
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