Research workbench
Actinonin bound crystal structure of class I type a peptide deformylase from acinetobacter baumannii
Analyse Actinonin bound crystal structure of class I type a peptide deformylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JET
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- A0A0J1A8B1
- Ligands
- BB2, ZN
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 170 | 37% helix, 32% strand | A0A0J1A8B1 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 171 | 36% helix, 30% strand | A0A0J1A8B1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.58 | 0.76 | 47 | BB2 |
| 2 | 117 | 0.50 | 0.81 | 20 | BB2 |
| 3 | 203 | 0.44 | 0.73 | 23 | empty |
| 4 | 115 | 0.39 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 368 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JET · Actinonin bound crystal structure of class I type a peptide deformylase from… · 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 A0A0J1A8B1
- Elsewhere: RCSB PDB 6JET · PDBe 6JET · UniProt A0A0J1A8B1
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