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Structure of the periplasmic binding protein (pbp) noct from A.TUMEFACIENS C58 in complex with histopine.
Analyse Structure of the periplasmic binding protein (pbp) noct from A.TUMEFACIENS C58… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OT9
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nopaline-binding periplasmic protein
- UniProt
- P35120
- Ligands
- AOZ
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nopaline-binding periplasmic protein | protein | 254 | 41% helix, 23% strand | P35120 |
| B | Nopaline-binding periplasmic protein | protein | 253 | 41% helix, 23% strand | P35120 |
Ligands and binding sites
- AOZ · Histopine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.70 | 0.93 | 28 | AOZ |
| 2 | 83 | 0.69 | 0.94 | 30 | AOZ |
| 3 | 721 | 0.68 | 0.76 | 55 | empty |
| 4 | 57 | 0.28 | 0.75 | 14 | empty |
| 5 | 52 | 0.27 | 0.74 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 678 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- P35120 · AlphaFold monomer V2.0 prediction for nopaline-binding periplasmic protein (P35120) · 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 P35120
- Elsewhere: RCSB PDB 5OT9 · PDBe 5OT9 · UniProt P35120
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