MolNFT v1 · #125464 · protein
Crystal structure of agrobacterium tumefaciens C58 strain pbp soca in complex with glucopine
5L9O · Deoxyfructosyl-amino acid transporter periplasmic binding…: “Crystal structure of agrobacterium tumefaciens C58 strain pbp soca in complex with glucopine”. X-ray diffraction, 2 ligands (GOP, CA), 5 pockets (best druggability 0.77).…
- PDB
- 5L9O
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyfructosyl-amino acid transporter periplasmic binding protein
- UniProt
- Q7D447
- Ligands
- GOP, CA
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyfructosyl-amino acid transporter periplasmic binding protein | protein | 241 | 37% helix, 23% strand | Q7D447 |
| B | Deoxyfructosyl-amino acid transporter periplasmic binding protein | protein | 243 | 37% helix, 23% strand | Q7D447 |
Ligands and binding sites
- GOP · Glucopine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
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 | 179 | 0.77 | 0.93 | 39 | GOP, EDO |
| 2 | 175 | 0.77 | 0.93 | 38 | GOP, EDO |
| 3 | 310 | 0.69 | 0.83 | 33 | empty |
| 4 | 108 | 0.38 | 0.75 | 16 | empty |
| 5 | 78 | 0.33 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5L9O · Crystal structure of Agrobacterium tumefaciens C58 strain PBP SocA in complex with… · the same entry in another collection · 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 Q7D447
- Elsewhere: RCSB PDB 5L9O · PDBe 5L9O · UniProt Q7D447
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