Research workbench
Crystal structure of human aspartyl aminopeptidase (dnpep) in complex with aspartic acid hydroxamate
Analyse Crystal structure of human aspartyl aminopeptidase (dnpep) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DYO
- Type
- protein
- Length
- 457 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartyl aminopeptidase
- EC
- 3.4.11.21
- UniProt
- Q9ULA0
- Ligands
- SD4, ZN, MG
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartyl aminopeptidase (EC 3.4.11.21) | protein | 457 | 32% helix, 25% strand | Q9ULA0 |
Ligands and binding sites
- SD4 · N-hydroxy-L-asparagine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · 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 | 254 | 0.54 | 0.76 | 34 | SD4 |
| 2 | 66 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 4DYO · Crystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in complex with Aspartic acid… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ULA0 · AlphaFold monomer V2.0 prediction for aspartyl aminopeptidase (Q9ULA0) · 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 Q9ULA0
- Elsewhere: RCSB PDB 4DYO · PDBe 4DYO · UniProt Q9ULA0
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