Research workbench
Crystals of peptide deformylase from plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design
Analyse Crystals of peptide deformylase from plasmodium falciparum with ten subunits… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JYM
- Type
- protein
- Length
- 1,736 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.31
- UniProt
- Q8I372
- Ligands
- CO
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.31) | protein | 179 | 30% helix, 27% strand | Q8I372 |
| C | Peptide deformylase (EC 3.5.1.31) | protein | 168 | 29% helix, 32% strand | Q8I372 |
| D, H | Peptide deformylase (EC 3.5.1.31) | protein | 173 | 31% helix, 30% strand | Q8I372 |
| E | Peptide deformylase (EC 3.5.1.31) | protein | 176 | 30% helix, 30% strand | Q8I372 |
| F | Peptide deformylase (EC 3.5.1.31) | protein | 172 | 33% helix, 31% strand | Q8I372 |
| G, I, J | Peptide deformylase (EC 3.5.1.31) | protein | 172 | 30% helix, 31% 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
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.82 | 0.83 | 118 | empty |
| 2 | 472 | 0.71 | 0.81 | 65 | empty |
| 3 | 552 | 0.70 | 0.79 | 67 | empty |
| 4 | 90 | 0.53 | 0.84 | 16 | empty |
| 5 | 75 | 0.52 | 0.84 | 16 | empty |
Interfaces
15 interfaces between chains.
- A–D · 790 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 736 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 608 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 521 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 466 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 1JYM · 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 1JYM · PDBe 1JYM · UniProt Q8I372
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