Research workbench
Crystal structure of an efpdf complex with met-ala-ser
Analyse Crystal structure of an efpdf complex with met-ala-ser in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G6N
- Type
- protein
- Length
- 372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase; Peptide (MET)(ALA)(SER)
- EC
- 3.5.1.88
- UniProt
- Q842S4
- Ligands
- NA, FE
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 183 | 28% helix, 26% strand | Q842S4 |
| F, G | Peptide (MET)(ALA)(SER) | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.45 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 549 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 296 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 292 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3G6N · Crystal structure of an EfPDF complex with Met-Ala-Ser · 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 3G6N · PDBe 3G6N · UniProt Q842S4
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