Research workbench
Peptide deformylase as ZN2+ containing form in complex with tripeptide met-ala-ser
Analyse Peptide deformylase as ZN2+ containing form in complex with tripeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BS8
- Type
- protein
- Length
- 513 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (peptide deformylase); Protein (met-ala-ser)
- EC
- 3.5.1.31
- UniProt
- P0A6K3
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein (peptide deformylase) (EC 3.5.1.31) | protein | 168 | 35% helix, 29% strand | P0A6K3 |
| D, E, F | Protein (met-ala-ser) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, D, B, E, C, F
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.44 | 0.75 | 19 | empty |
| 2 | 136 | 0.39 | 0.73 | 21 | empty |
| 3 | 94 | 0.33 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–C · 612 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 342 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 323 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 322 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1BS8 · Peptide deformylase as ZN2+ containing form in complex with tripeptide met-ala-ser · the same entry in another collection · chain C against C, TM-score 1.00
- P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A6K3
- Elsewhere: RCSB PDB 1BS8 · PDBe 1BS8 · UniProt P0A6K3
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