Research workbench
Structure of the periplasmic binding protein noct from A.TUMEFACIENS in complex with octopine
Analyse Structure of the periplasmic binding protein noct from A.TUMEFACIENS in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.