Research workbench
Structure of the periplasmic binding protein (pbp) occj from agrobacterium tumefaciens B6
Analyse Structure of the periplasmic binding protein (pbp) occj from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ORE
- Type
- protein
- Length
- 261 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octopine-binding periplasmic protein
- UniProt
- P0A4F8
- Ligands
- CL
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Octopine-binding periplasmic protein | protein | 261 | 39% helix, 25% strand | P0A4F8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.52 | 0.78 | 28 | empty |
Compared structures
- P0A4F8 · AlphaFold monomer V2.0 prediction for octopine-binding periplasmic protein (P0A4F8) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 5ORE · PDBe 5ORE · UniProt P0A4F8
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