MolNFT v1 · #60257 · protein
Crystal structure of peptide deformylase from vre-E.FAECIUM
3CMD: “Crystal structure of peptide deformylase from vre-E.FAECIUM”. X-ray diffraction, 2 ligands (NA, FE), 2 pockets (best druggability 0.59). MolNFT v1 #60257 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CMD
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q842S4
- Ligands
- NA, FE
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 186 | 28% helix, 25% strand | Q842S4 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 188 | 28% helix, 27% strand | Q842S4 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- MLI · Malonate ion · additive · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.59 | 0.84 | 26 | FE, NA, MLI |
| 2 | 97 | 0.50 | 0.82 | 19 | FE, NA, MLI |
Interfaces
1 interface between chains.
- A–B · 831 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3CMD · Crystal structure of peptide deformylase from VRE-E.faecium · 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 Q842S4
- Elsewhere: RCSB PDB 3CMD · PDBe 3CMD · UniProt Q842S4
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