Research workbench
K1U bound crystal structure of class I type B peptide deformylase from acinetobacter baumannii
Analyse K1U 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
- 6JF4
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- A0A098SKQ8
- Ligands
- K1U, ZN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Peptide deformylase (EC 3.5.1.88) | protein | 153 | 29% helix, 35% strand | A0A098SKQ8 |
| A | Peptide deformylase (EC 3.5.1.88) | protein | 148 | 29% helix, 32% strand | A0A098SKQ8 |
Ligands and binding sites
- K1U · (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl) sulfanyl]butanoic acid · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.55 | 0.79 | 33 | K1U |
| 2 | 103 | 0.50 | 0.82 | 19 | K1U |
Interfaces
1 interface between chains.
- B–A · 946 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6JF4 · K1U bound crystal structure of class I type b peptide deformylase from Acinetobacter… · the same entry in another collection · chain B against B, 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 A0A098SKQ8
- Elsewhere: RCSB PDB 6JF4 · PDBe 6JF4 · UniProt A0A098SKQ8
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