Research workbench
K3U bound crystal structure of class II peptide deformylase from methicillin resistant staphylococcus aureus
Analyse K3U bound crystal structure of class II peptide deformylase from methicillin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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