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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 v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Renal dipeptidase
EC
3.4.13.19
UniProt
P16444
Ligands
NAG, ZN
Pockets
7 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BRenal dipeptidase (EC 3.4.13.19)protein36944% helix, 14% strandP16444

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1640.730.9921empty
2660.720.9821empty
31540.480.7717empty
41360.470.7821empty
5760.370.7719ZN

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

  • 1ITQ · Human renal dipeptidase · the same entry in another collection · chain A against A, TM-score 1.00
  • P16444 · AlphaFold monomer V2.0 prediction for dipeptidase 1 (P16444) · a predicted model of the same protein · chain B against A, TM-score 1.00

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