MolNFT v1 · #11842 · protein
Crystals of peptide deformylase from plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design
1JYM: “Crystals of peptide deformylase from plasmodium falciparum with ten subunits per asymmetric unit reveal…”. X-ray diffraction, 1 ligand (CO), 20 pockets (best druggability 0.82). MolNFT v1 #11842 on GenesisL1: 3D structure, binding…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.