Research workbench
Human renal dipeptidase
Analyse Human renal dipeptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ITQ
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- Renal dipeptidase
- EC
- 3.4.13.19
- UniProt
- P16444
- Ligands
- NAG, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renal dipeptidase (EC 3.4.13.19) | protein | 369 | 44% helix, 14% strand | P16444 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.73 | 0.99 | 21 | empty |
| 2 | 66 | 0.72 | 0.98 | 21 | empty |
| 3 | 154 | 0.48 | 0.77 | 17 | empty |
| 4 | 136 | 0.47 | 0.78 | 21 | empty |
| 5 | 76 | 0.37 | 0.77 | 19 | ZN |
Interfaces
1 interface between chains.
- A–B · 2202 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 P16444
- Elsewhere: RCSB PDB 1ITQ · PDBe 1ITQ · UniProt P16444
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