MolNFT v1 · #153467 · protein
Actinonin bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa
6JFC: “Actinonin bound crystal structure of class I type B peptide deformylase from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (BB2, NI), 6 pockets (best druggability 0.64). MolNFT v1 #153467 on GenesisL1: 3D structure, binding…
- PDB
- 6JFC
- Type
- protein
- Length
- 321 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
- BB2, NI
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 160 | 29% helix, 34% strand | A0A1C7BES9 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 161 | 32% helix, 34% strand | A0A1C7BES9 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 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 | 247 | 0.64 | 0.82 | 36 | empty |
| 2 | 239 | 0.61 | 0.81 | 31 | empty |
| 3 | 144 | 0.49 | 0.79 | 19 | BB2 |
| 4 | 102 | 0.48 | 0.81 | 18 | BB2, NI |
| 5 | 78 | 0.33 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 503 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6JFC · Actinonin 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 6JFC · PDBe 6JFC · UniProt A0A1C7BES9
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