MolNFT v1 · #153482 · protein
K3U bound crystal structure of class II peptide deformylase from methicillin resistant staphylococcus aureus
6JFR: “K3U bound crystal structure of class II peptide deformylase from methicillin resistant staphylococcus aureus”. X-ray diffraction, 2 ligands (K3U, NI), 1 pocket (best druggability 0.54). MolNFT v1 #153482 on GenesisL1: 3D structure…
- PDB
- 6JFR
- Type
- protein
- Length
- 183 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- P68826
- Ligands
- K3U, NI
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 183 | 27% helix, 25% strand | P68826 |
Ligands and binding sites
- K3U · S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.54 | 0.83 | 18 | NI, K3U |
Compared structures
- 6JFR · K3U bound crystal structure of class II peptide deformylase from methicillin resistant… · the same entry in another collection · chain A against A, TM-score 1.00
- P68826 · AlphaFold monomer V2.0 prediction for peptide deformylase (P68826) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P68826
- Elsewhere: RCSB PDB 6JFR · PDBe 6JFR · UniProt P68826
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