MolNFT v1 · #122584 · protein
Structure of the periplasmic binding protein M117N-noct from a. tumefaciens in complex with octopine
5ITO · Nopaline-binding periplasmic protein: “Structure of the periplasmic binding protein M117N-noct from a. tumefaciens in complex with octopine”. X-ray diffraction, 2 ligands (6DB, TOE), 5 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5ITO
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nopaline-binding periplasmic protein
- UniProt
- P35120
- Ligands
- 6DB, TOE
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nopaline-binding periplasmic protein | protein | 255 | 39% helix, 23% strand | P35120 |
| B | Nopaline-binding periplasmic protein | protein | 255 | 40% helix, 23% strand | P35120 |
Ligands and binding sites
- 6DB · octopine · ligand · 2 copies · chains A, B
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- 1PE · Pentaethylene glycol · 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 | 806 | 0.72 | 0.77 | 54 | EDO |
| 2 | 104 | 0.72 | 0.94 | 31 | 6DB |
| 3 | 124 | 0.69 | 0.91 | 34 | 6DB |
| 4 | 54 | 0.30 | 0.76 | 15 | EDO |
| 5 | 51 | 0.26 | 0.74 | 16 | 1PE |
Interfaces
1 interface between chains.
- A–B · 685 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5ITO · Structure of the periplasmic binding protein M117N-NocT from A. tumefaciens in complex… · 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 B 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 5ITO · PDBe 5ITO · UniProt P35120
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