MolNFT v1 · #125457 · protein
Crystal structure of the pbp mota in complex with mannopine from a. tumefaciens B6
5L9G · Periplasmic binding protein: “Crystal structure of the pbp mota in complex with mannopine from a. tumefaciens B6”. X-ray diffraction, 2 ligands (MO0, CA), 7 pockets (best druggability 0.79). MolNFT v1 #125457 on GenesisL1: 3D…
- PDB
- 5L9G
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding protein
- UniProt
- A0A109C781
- Ligands
- MO0, CA
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic binding protein | protein | 325 | 45% helix, 21% strand | A0A109C781 |
| B | Periplasmic binding protein | protein | 324 | 44% helix, 21% strand | A0A109C781 |
Ligands and binding sites
- MO0 · mannopine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.79 | 0.96 | 32 | MO0 |
| 2 | 136 | 0.79 | 0.96 | 32 | MO0, CA |
| 3 | 54 | 0.38 | 0.80 | 17 | EDO |
| 4 | 69 | 0.35 | 0.77 | 20 | EDO |
| 5 | 79 | 0.33 | 0.74 | 24 | CA |
Interfaces
1 interface between chains.
- A–B · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5L9G · Crystal Structure of the PBP MotA in complex with mannopine from A. tumefaciens B6 · 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 A0A109C781
- Elsewhere: RCSB PDB 5L9G · PDBe 5L9G · UniProt A0A109C781
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