MolNFT v1 · #125462 · protein
Crystal structure of the pbp mota from a. tumefaciens B6 in complex with glucopine
5L9L · Periplasmic binding protein: “Crystal structure of the pbp mota from a. tumefaciens B6 in complex with glucopine”. X-ray diffraction, 2 ligands (GOP, CA), 8 pockets (best druggability 0.80). MolNFT v1 #125462 on GenesisL1: 3D…
- PDB
- 5L9L
- Type
- protein
- Length
- 645 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding protein
- UniProt
- A0A109C781
- Ligands
- GOP, CA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic binding protein | protein | 323 | 45% helix, 20% strand | A0A109C781 |
| B | Periplasmic binding protein | protein | 322 | 45% helix, 20% strand | A0A109C781 |
Ligands and binding sites
- GOP · Glucopine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.80 | 0.97 | 31 | GOP |
| 2 | 259 | 0.74 | 0.88 | 51 | GOP |
| 3 | 316 | 0.62 | 0.79 | 45 | CA |
| 4 | 254 | 0.53 | 0.76 | 32 | CA, EDO |
| 5 | 203 | 0.48 | 0.76 | 27 | CA |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5L9L · Crystal structure of the PBP MotA from A. tumefaciens B6 in complex with glucopine · 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 5L9L · PDBe 5L9L · UniProt A0A109C781
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