MolNFT v1 · #153461 · protein
Met-ala-ser bound crystal structure of class I type B peptide deformylase from acinetobacter baumannii
6JF6: “Met-ala-ser bound crystal structure of class I type B peptide deformylase from acinetobacter baumannii”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #153461 on GenesisL1: 3D structure, binding…
- PDB
- 6JF6
- Type
- protein
- Length
- 634 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase; Met-ala-ser
- EC
- 3.5.1.88
- UniProt
- A0A0E1FIJ3
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Peptide deformylase (EC 3.5.1.88) | protein | 159 | 28% helix, 30% strand | A0A0E1FIJ3 |
| D | Peptide deformylase (EC 3.5.1.88) | protein | 154 | 27% helix, 31% strand | A0A0E1FIJ3 |
| E | Met-ala-ser | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.68 | 0.77 | 58 | empty |
| 2 | 169 | 0.60 | 0.83 | 30 | empty |
| 3 | 135 | 0.59 | 0.84 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1027 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 978 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 354 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6JF6 · Met-ala-ser bound crystal structure of class I type b 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 A0A0E1FIJ3
- Elsewhere: RCSB PDB 6JF6 · PDBe 6JF6 · UniProt A0A0E1FIJ3
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