Research workbench
Crystal structure of E.COLI polypeptide deformylase complexed with the inhibitor bb-3497
Analyse Crystal structure of E.COLI polypeptide deformylase complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G27
- Type
- protein
- Length
- 492 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polypeptide deformylase
- EC
- 3.5.1.31
- UniProt
- P0A6K3
- Ligands
- BB1, NI
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Polypeptide deformylase (EC 3.5.1.31) | protein | 164 | 35% helix, 27% strand | P0A6K3 |
Ligands and binding sites
- BB1 · 2-[(formyl-hydroxy-amino)-methyl]-hexanoic acid (1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.54 | 0.76 | 36 | BB1 |
| 2 | 152 | 0.51 | 0.79 | 26 | BB1 |
| 3 | 138 | 0.50 | 0.80 | 23 | BB1 |
| 4 | 129 | 0.42 | 0.75 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 578 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1G27 · Crystal structure of E.COLI polypeptide deformylase complexed with the inhibitor bb-3497 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 1G27 · PDBe 1G27 · UniProt P0A6K3
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