Research workbench
The structure of E.COLI peptide deformylase (pdf) in complex with peptidomimetic ligand BB2827
Analyse The structure of E.COLI peptide deformylase (pdf) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K6L
- Type
- protein
- Length
- 481 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- P0A6K3
- Ligands
- 2BB, NI
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 164 | 34% helix, 32% strand | P0A6K3 |
| C | Peptide deformylase (EC 3.5.1.88) | protein | 153 | 33% helix, 27% strand | P0A6K3 |
Ligands and binding sites
- 2BB · (2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide · ligand · 2 copies · chains A, B
- 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.75 | 0.78 | 96 | 2BB |
| 2 | 268 | 0.61 | 0.80 | 25 | empty |
| 3 | 144 | 0.52 | 0.80 | 24 | NI |
| 4 | 152 | 0.51 | 0.79 | 22 | 2BB |
| 5 | 155 | 0.44 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 561 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 489 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 145 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3K6L · The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand… · 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 3K6L · PDBe 3K6L · UniProt P0A6K3
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