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K3U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
Analyse K3U bound crystal structure of class I type b peptide deformylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JF7
- Type
- protein
- Length
- 303 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Acinetobacter baumannii
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- A0A0E1FIJ3
- Ligands
- K3U, ZN
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 151 | 30% helix, 31% strand | A0A0E1FIJ3 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 152 | 30% helix, 31% strand | A0A0E1FIJ3 |
Ligands and binding sites
- K3U · S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.57 | 0.80 | 31 | K3U |
| 2 | 170 | 0.51 | 0.78 | 29 | K3U |
Interfaces
1 interface between chains.
- A–B · 931 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6JF7 · K3U bound crystal structure of class I type B peptide deformylase from acinetobacter… · 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 A0A0E1FIJ3
- Elsewhere: RCSB PDB 6JF7 · PDBe 6JF7 · UniProt A0A0E1FIJ3
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