Research workbench
Crystal structure of the PBP MotA from A. tumefaciens B6
Analyse Crystal structure of the PBP MotA from A. tumefaciens B6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L9P
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.54
- Source
- Agrobacterium tumefaciens str. B6
- Molecule
- periplasmic binding protein
- UniProt
- A0A109C781
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.54 · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | periplasmic binding protein | protein | 340 | 45% helix, 20% strand | A0A109C781 |
| B | periplasmic binding protein | protein | 342 | 44% helix, 20% strand | A0A109C781 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.64 | 0.77 | 60 | SO4 |
| 2 | 475 | 0.63 | 0.76 | 56 | empty |
| 3 | 418 | 0.61 | 0.76 | 53 | empty |
| 4 | 191 | 0.46 | 0.74 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–B · 712 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5L9P · Crystal structure of the pbp mota 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 5L9P · PDBe 5L9P · UniProt A0A109C781
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