MolNFT v1 · #103916 · protein
Proline aminopeptidase P II from yersinia pestis
4PV4: “Proline aminopeptidase P II from yersinia pestis”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.83). MolNFT v1 #103916 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PV4
- Type
- protein
- Length
- 872 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline aminopeptidase P II
- EC
- 3.4.11.9
- UniProt
- Q7CGS9
- Ligands
- MG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proline aminopeptidase P II (EC 3.4.11.9) | protein | 436 | 39% helix, 19% strand | Q7CGS9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains A
- P6G · Hexaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.83 | 0.95 | 40 | empty |
| 2 | 972 | 0.79 | 0.81 | 77 | 1PE |
| 3 | 919 | 0.78 | 0.81 | 72 | P6G, EDO |
| 4 | 125 | 0.45 | 0.77 | 29 | empty |
| 5 | 103 | 0.43 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2104 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4PV4 · Proline aminopeptidase P II from Yersinia pestis · 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 Q7CGS9
- Elsewhere: RCSB PDB 4PV4 · PDBe 4PV4 · UniProt Q7CGS9
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