Research workbench
Crystal structure of human carnosine dipeptidase 1
Analyse Crystal structure of human carnosine dipeptidase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DLJ
- Type
- protein
- Length
- 938 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-ala-his dipeptidase
- EC
- 3.4.13.20
- UniProt
- Q96KN2
- Ligands
- ZN, UNX, SO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-ala-his dipeptidase (EC 3.4.13.20) | protein | 471 | 36% helix, 23% strand | Q96KN2 |
| B | Beta-ala-his dipeptidase (EC 3.4.13.20) | protein | 467 | 36% helix, 23% strand | Q96KN2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- UNX · Unknown atom or ion · ion · 15 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.75 | 0.80 | 98 | UNX |
| 2 | 64 | 0.70 | 0.97 | 27 | empty |
| 3 | 53 | 0.69 | 0.98 | 22 | UNX |
| 4 | 63 | 0.60 | 0.91 | 26 | empty |
| 5 | 85 | 0.60 | 0.88 | 24 | UNX |
Interfaces
1 interface between chains.
- A–B · 3627 Ų buried · 58 hydrogen bonds · protein-protein
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 Q96KN2
- Elsewhere: RCSB PDB 3DLJ · PDBe 3DLJ · UniProt Q96KN2
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