Research workbench
Plasmodium falciparum peptide deformylase complex with inhibitor
Analyse Plasmodium falciparum peptide deformylase complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RL4
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylmethionine deformylase
- EC
- 3.5.1.31
- UniProt
- Q8I372
- Ligands
- BRR, BL5, CO
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formylmethionine deformylase (EC 3.5.1.31) | protein | 154 | 38% helix, 29% strand | Q8I372 |
| B | Formylmethionine deformylase (EC 3.5.1.31) | protein | 156 | 38% helix, 28% strand | Q8I372 |
Ligands and binding sites
- BRR · (2R)-2-{[formyl(hydroxy)amino]methyl}hexanoic acid · ligand · 2 copies · chains A, B
- BL5 · 2-{N'-[2-(5-amino-1-phenylcarbamoyl-pentylcarbamoyl)-hexyl]-hydrazinomethyl}-hexanoic acid(5-amino-1-phenylcarbamoyl-pentyl)-amide · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.45 | 0.78 | 17 | BRR |
| 2 | 103 | 0.43 | 0.78 | 19 | CO, BRR |
Interfaces
1 interface between chains.
- A–B · 609 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1RL4 · Plasmodium falciparum peptide deformylase complex with inhibitor · 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 Q8I372
- Elsewhere: RCSB PDB 1RL4 · PDBe 1RL4 · UniProt Q8I372
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