MolNFT v1 · #153478 · protein
K4U bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa
6JFN: “K4U bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (LHY, NI), 6 pockets (best druggability 0.64). MolNFT v1 #153478 on GenesisL1: 3D structure, binding sites…
- PDB
- 6JFN
- Type
- protein
- Length
- 325 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
- LHY, NI
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 166 | 31% helix, 33% strand | A0A1C7BES9 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 159 | 29% helix, 31% strand | A0A1C7BES9 |
Ligands and binding sites
- LHY · L-[(N-hydroxyamino)carbonyl]phenylalanine · ligand · chains B
- NI · Nickel (II) ion · metal · 3 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 | 282 | 0.64 | 0.81 | 36 | empty |
| 2 | 194 | 0.57 | 0.80 | 30 | empty |
| 3 | 98 | 0.48 | 0.81 | 17 | LHY |
| 4 | 115 | 0.45 | 0.78 | 21 | empty |
| 5 | 82 | 0.34 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6JFN · K4U 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 6JFN · PDBe 6JFN · UniProt A0A1C7BES9
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