MolNFT v1 · #20801 · protein
Crystals of peptide deformylase from plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design
1RQC · Formylmethionine deformylase: “Crystals of peptide deformylase from plasmodium falciparum with ten subunits per asymmetric unit reveal…”. X-ray diffraction, 1 ligand (CO), 16 pockets (best druggability 0.78). MolNFT v1 #20801 on…
- PDB
- 1RQC
- Type
- protein
- Length
- 1,730 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylmethionine deformylase
- UniProt
- Q8I372
- Ligands
- CO
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formylmethionine deformylase | protein | 178 | 33% helix, 31% strand | Q8I372 |
| C | Formylmethionine deformylase | protein | 168 | 37% helix, 28% strand | Q8I372 |
| D, H | Formylmethionine deformylase | protein | 173 | 31% helix, 27% strand | Q8I372 |
| E | Formylmethionine deformylase | protein | 175 | 35% helix, 27% strand | Q8I372 |
| F | Formylmethionine deformylase | protein | 172 | 33% helix, 26% strand | Q8I372 |
| G, I, J | Formylmethionine deformylase | protein | 171 | 33% helix, 27% strand | Q8I372 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.78 | 0.82 | 97 | empty |
| 2 | 102 | 0.74 | 0.95 | 25 | empty |
| 3 | 99 | 0.72 | 0.94 | 23 | empty |
| 4 | 468 | 0.70 | 0.81 | 64 | empty |
| 5 | 247 | 0.69 | 0.85 | 39 | empty |
Interfaces
10 interfaces between chains.
- B–C · 846 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 774 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 695 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 649 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 623 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 1RQC · Crystals of peptide deformylase from Plasmodium falciparum with ten subunits per… · 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 1RQC · PDBe 1RQC · UniProt Q8I372
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