MolNFT v1 · #68790 · protein
The structure of E.COLI peptide deformylase (pdf) in complex with peptidomimetic ligand BB2827
3K6L: “The structure of E.COLI peptide deformylase (pdf) in complex with peptidomimetic ligand BB2827”. X-ray diffraction, 2 ligands (2BB, NI), 6 pockets (best druggability 0.75). MolNFT v1 #68790 on GenesisL1: 3D structure, binding sites…
- 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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