MolNFT v1 · #153470 · protein
K3U bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa
6JFF: “K3U bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (K3U, NI), 6 pockets (best druggability 0.63). MolNFT v1 #153470 on GenesisL1: 3D structure, binding sites…
- PDB
- 6JFF
- Type
- protein
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- A0A1C7BES9
- Ligands
- K3U, NI
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 160 | 31% helix, 36% strand | A0A1C7BES9 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 157 | 31% helix, 33% strand | A0A1C7BES9 |
Ligands and binding sites
- K3U · S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate · ligand · chains B
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.63 | 0.82 | 29 | empty |
| 2 | 162 | 0.59 | 0.82 | 29 | empty |
| 3 | 87 | 0.44 | 0.80 | 19 | empty |
| 4 | 82 | 0.41 | 0.79 | 20 | K3U |
| 5 | 82 | 0.32 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6JFF · K3U bound crystal structure of class I type b peptide deformylase from Pseudomonas… · 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 A0A1C7BES9
- Elsewhere: RCSB PDB 6JFF · PDBe 6JFF · UniProt A0A1C7BES9
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