Research workbench
Crystal structure of leucyl aminopeptidase (pepa) from XOO0834, xanthomonas oryzae pv. oryzae KACC10331
Analyse Crystal structure of leucyl aminopeptidase (pepa) from XOO0834, xanthomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JRU
- Type
- protein
- Length
- 980 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable cytosol aminopeptidase
- EC
- 3.4.11.1
- UniProt
- Q5H4N2
- Ligands
- ZN, CA, CO3
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Probable cytosol aminopeptidase (EC 3.4.11.1) | protein | 490 | 39% helix, 20% strand | Q5H4N2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
- CO3 · Carbonate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.68 | 0.79 | 47 | empty |
| 2 | 460 | 0.67 | 0.79 | 39 | empty |
| 3 | 475 | 0.67 | 0.79 | 43 | CO3 |
| 4 | 457 | 0.65 | 0.78 | 45 | CO3 |
| 5 | 77 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 1249 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3JRU · Crystal structure of Leucyl Aminopeptidase (pepA) from Xoo0834,Xanthomonas oryzae pv.… · the same entry in another collection · chain B against B, TM-score 1.00
- Q5H4N2 · AlphaFold monomer V2.0 prediction for probable cytosol aminopeptidase (Q5H4N2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5H4N2
- Elsewhere: RCSB PDB 3JRU · PDBe 3JRU · UniProt Q5H4N2
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