MolNFT v1 · #56846 · protein
Crystal structure of X-pro aminopeptidase from thermotoga maritima MSB8
2ZSG · Aminopeptidase P, putative: “Crystal structure of X-pro aminopeptidase from thermotoga maritima MSB8”. X-ray diffraction, 3 ligands (NA, ZN, CL), 6 pockets (best druggability 0.77). MolNFT v1 #56846 on GenesisL1: 3D structure…
- PDB
- 2ZSG
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase P, putative
- EC
- 3.4.11.9
- UniProt
- Q9WXP9
- Ligands
- NA, ZN, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase P, putative (EC 3.4.11.9) | protein | 356 | 38% helix, 26% strand | Q9WXP9 |
| B | Aminopeptidase P, putative (EC 3.4.11.9) | protein | 352 | 38% helix, 25% strand | Q9WXP9 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.77 | 0.85 | 74 | ZN |
| 2 | 273 | 0.67 | 0.83 | 37 | empty |
| 3 | 214 | 0.62 | 0.82 | 27 | empty |
| 4 | 137 | 0.60 | 0.85 | 23 | empty |
| 5 | 243 | 0.53 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1592 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2ZSG · Crystal structure of X-Pro aminopeptidase from Thermotoga maritima MSB8 · 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 Q9WXP9
- Elsewhere: RCSB PDB 2ZSG · PDBe 2ZSG · UniProt Q9WXP9
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