Research workbench
Structure of the periplasmic binding protein (pbp) noct-G97S mutant from a. tumefaciens C58 in complex with octopine.
Analyse Structure of the periplasmic binding protein (pbp) noct-G97S mutant from a.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OT8
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nopaline-binding periplasmic protein
- UniProt
- P35120
- Ligands
- 6DB, CL, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nopaline-binding periplasmic protein | protein | 256 | 39% helix, 23% strand | P35120 |
| B | Nopaline-binding periplasmic protein | protein | 255 | 39% helix, 23% strand | P35120 |
Ligands and binding sites
- 6DB · octopine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 90 | 0.72 | 0.95 | 27 | 6DB, EDO |
| 2 | 849 | 0.71 | 0.76 | 57 | empty |
| 3 | 85 | 0.69 | 0.93 | 30 | CL, 6DB |
| 4 | 50 | 0.25 | 0.73 | 15 | empty |
| 5 | 50 | 0.24 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 643 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5OT8 · Structure of the periplasmic binding protein (PBP) NocT-G97S mutant from A. tumefaciens… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 5OT8 · PDBe 5OT8 · UniProt P35120
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