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Structure of the periplasmic binding protein (pbp) occj from a. tumefaciens B6 in complex with octopine.
Analyse Structure of the periplasmic binding protein (pbp) occj from a. tumefaciens B6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
- 5ORG · Structure of the periplasmic binding protein (PBP) OccJ from A. tumefaciens B6 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- 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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