MolNFT v1 · #79176 · protein
Strep peptide deformylase with a time dependent thiazolidine amide
3SVJ · Peptide deformylase 3: “Strep peptide deformylase with a time dependent thiazolidine amide”. X-ray diffraction, 3 ligands (4LI, NI, SO4), 1 pocket (best druggability 0.54). MolNFT v1 #79176 on GenesisL1: 3D structure, binding sites…
- PDB
- 3SVJ
- Type
- protein
- Length
- 193 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase 3
- EC
- 3.5.1.88
- UniProt
- Q939R9
- Ligands
- 4LI, NI, SO4
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Peptide deformylase 3 (EC 3.5.1.88) | protein | 193 | 30% helix, 26% strand | Q939R9 |
Ligands and binding sites
- 4LI · (4R)-3-(4-[4-(2-chlorophenyl)piperazin-1-yl]-6-{[2-methyl-6-(methylcarbamoyl)phenyl]amino}-1,3,5-triazin-2-yl)-N-methyl-1,3-thiazolidine-4-carboxamide · ligand · chains P
- NI · Nickel (II) ion · metal · chains P
- SO4 · Sulfate ion · ion · 3 copies · chains P
- GOL · Glycerol · additive · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.54 | 0.80 | 20 | 4LI |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 3SVJ · Strep Peptide Deformylase with a time dependent thiazolidine amide · the same entry in another collection · chain P against P, 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 Q939R9
- Elsewhere: RCSB PDB 3SVJ · PDBe 3SVJ · UniProt Q939R9
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