MolNFT v1 · #75070 · protein
Crystal structure of a M20A metallo peptidase (dape, LPG0809) from legionella pneumophila subsp. pneumophila str. philadelphia 1 at 1.50 a resolution
3PFE · Succinyl-diaminopimelate desuccinylase: “Crystal structure of a M20A metallo peptidase (dape, LPG0809) from legionella pneumophila subsp. pneumophila…”. X-ray diffraction, 2 ligands (ZN, CL), 2 pockets (best druggability 0.75).…
- PDB
- 3PFE
- Type
- protein
- Length
- 471 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-diaminopimelate desuccinylase
- UniProt
- Q5ZXC3
- Ligands
- ZN, CL
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-diaminopimelate desuccinylase | protein | 471 | 40% helix, 23% strand | Q5ZXC3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
- CL · Chloride ion · ion · 8 copies · chains A
- GOL · Glycerol · additive · 10 copies · chains A
- IMD · Imidazole · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 916 | 0.75 | 0.79 | 83 | ZN, CL, IMD, GOL |
| 2 | 51 | 0.27 | 0.74 | 13 | GOL |
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3PFE · Crystal structure of a M20A metallo peptidase (dapE, lpg0809) from Legionella pneumophila… · 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 Q5ZXC3
- Elsewhere: RCSB PDB 3PFE · PDBe 3PFE · UniProt Q5ZXC3
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