MolNFT v1 · #122585 · protein
Structure of the periplasmic binding protein noct from A.TUMEFACIENS in complex with octopine
5ITP · Nopaline-binding periplasmic protein: “Structure of the periplasmic binding protein noct from A.TUMEFACIENS in complex with octopine”. X-ray diffraction, 1 ligand (6DB), 6 pockets (best druggability 0.71). MolNFT v1 #122585 on…
- PDB
- 5ITP
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nopaline-binding periplasmic protein
- UniProt
- P35120
- Ligands
- 6DB
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nopaline-binding periplasmic protein | protein | 254 | 39% helix, 23% strand | P35120 |
Ligands and binding sites
- 6DB · octopine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.71 | 0.76 | 53 | empty |
| 2 | 85 | 0.69 | 0.94 | 29 | 6DB, PEG |
| 3 | 95 | 0.68 | 0.92 | 28 | 6DB |
| 4 | 60 | 0.31 | 0.75 | 15 | empty |
| 5 | 69 | 0.29 | 0.73 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5ITP · Structure of the periplasmic binding protein NocT from A.tumefaciens in complex with… · the same entry in another collection · chain B against B, 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 5ITP · PDBe 5ITP · UniProt P35120
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