Research workbench
Crystal structure of human mitochondrial X-prolyl aminopeptidase (XPNPEP3)
Analyse Crystal structure of human mitochondrial X-prolyl aminopeptidase (XPNPEP3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X49
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable xaa-pro aminopeptidase 3
- EC
- 3.4.11.9
- UniProt
- Q9NQH7
- Ligands
- 01B, MN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable xaa-pro aminopeptidase 3 (EC 3.4.11.9) | protein | 441 | 40% helix, 20% strand | Q9NQH7 |
Ligands and binding sites
- 01B · (2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
- 12P · Dodecaethylene glycol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.82 | 0.84 | 101 | EDO |
| 2 | 229 | 0.73 | 0.88 | 31 | MN, 01B, DMS |
| 3 | 234 | 0.71 | 0.87 | 33 | 01B, DMS |
| 4 | 117 | 0.46 | 0.79 | 20 | empty |
| 5 | 84 | 0.42 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1605 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5X49 · Crystal Structure of Human mitochondrial X-prolyl Aminopeptidase (XPNPEP3) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQH7 · AlphaFold monomer V2.0 prediction for xaa-pro aminopeptidase 3 (Q9NQH7) · a predicted model of the same protein · 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 Q9NQH7
- Elsewhere: RCSB PDB 5X49 · PDBe 5X49 · UniProt Q9NQH7
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