MolNFT v1 · #129676 · protein
Structure of the periplasmic binding protein (pbp) occj from a. tumefaciens B6 in complex with octopine.
5ORG · Octopine-binding periplasmic protein: “Structure of the periplasmic binding protein (pbp) occj from a. tumefaciens B6 in complex with octopine.”. X-ray diffraction, 3 ligands (6DB, NA, CL), 7 pockets (best druggability 0.83). MolNFT…
- PDB
- 5ORG
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octopine-binding periplasmic protein
- UniProt
- P0A4F8
- Ligands
- 6DB, NA, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octopine-binding periplasmic protein | protein | 257 | 37% helix, 26% strand | P0A4F8 |
| B | Octopine-binding periplasmic protein | protein | 253 | 38% helix, 25% strand | P0A4F8 |
Ligands and binding sites
- 6DB · octopine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 9 copies · chains A, B
- CL · Chloride ion · ion · 14 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.83 | 0.90 | 50 | CL |
| 2 | 56 | 0.71 | 0.98 | 25 | 6DB |
| 3 | 55 | 0.70 | 0.98 | 23 | NA, 6DB |
| 4 | 171 | 0.51 | 0.78 | 26 | EDO |
| 5 | 67 | 0.30 | 0.74 | 22 | CL |
Interfaces
1 interface between chains.
- A–B · 889 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- P0A4F8 · AlphaFold monomer V2.0 prediction for octopine-binding periplasmic protein (P0A4F8) · a predicted model of the same protein · chain B 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 P0A4F8
- Elsewhere: RCSB PDB 5ORG · PDBe 5ORG · UniProt P0A4F8
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