MolNFT v1 · #153481 · protein
K2U bound crystal structure of class II peptide deformylase from methicillin resistant staphylococcus aureus
6JFQ: “K2U bound crystal structure of class II peptide deformylase from methicillin resistant staphylococcus aureus”. X-ray diffraction, 2 ligands (K2U, NI), 1 pocket (best druggability 0.52). MolNFT v1 #153481 on GenesisL1: 3D structure…
- PDB
- 6JFQ
- 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
- K2U, NI
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 183 | 28% helix, 25% strand | P68826 |
Ligands and binding sites
- K2U · (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid · ligand · chains A
- NI · Nickel (II) ion · metal · 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 | 121 | 0.52 | 0.82 | 19 | K2U |
Compared structures
- 6JFQ · K2U 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 6JFQ · PDBe 6JFQ · UniProt P68826
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