Research workbench
Crystal structure of Acinetobacter baumannii OccAB4
Analyse Crystal structure of Acinetobacter baumannii OccAB4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DL8
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Acinetobacter baumannii AB307-0294
- Molecule
- Benzoate transport porin BenP
- UniProt
- A0A0D5YI36
- Ligands
- CA
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 1% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Benzoate transport porin BenP | protein | 391 | 1% helix, 62% strand | A0A0D5YI36 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 8 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.75 | 0.79 | 119 | empty |
| 2 | 374 | 0.62 | 0.77 | 61 | empty |
| 3 | 210 | 0.58 | 0.80 | 30 | empty |
| 4 | 73 | 0.45 | 0.82 | 16 | empty |
| 5 | 72 | 0.44 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 564 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DL8 · Crystal structure of acinetobacter baumannii OCCAB4 · 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 A0A0D5YI36
- Elsewhere: RCSB PDB 5DL8 · PDBe 5DL8 · UniProt A0A0D5YI36
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