MolNFT v1 · #153450 · protein
K2U bound crystal structure of class I type a peptide deformylase from acinetobacter baumanii
6JEV: “K2U bound crystal structure of class I type a peptide deformylase from acinetobacter baumanii”. X-ray diffraction, 2 ligands (K2U, ZN), 2 pockets (best druggability 0.73). MolNFT v1 #153450 on GenesisL1: 3D structure, binding sites…
- PDB
- 6JEV
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- A0A0J1A8B1
- Ligands
- K2U, ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 171 | 38% helix, 27% strand | A0A0J1A8B1 |
Ligands and binding sites
- K2U · (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid · 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 | 831 | 0.73 | 0.78 | 85 | K2U |
| 2 | 195 | 0.53 | 0.78 | 33 | K2U |
Interfaces
1 interface between chains.
- A–B · 438 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6JEV · K2U bound crystal structure of class I type a 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 A0A0J1A8B1
- Elsewhere: RCSB PDB 6JEV · PDBe 6JEV · UniProt A0A0J1A8B1
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