Research workbench
Structure of K-26-dcp in complex with the K-26 tripeptide
Analyse Structure of K-26-dcp in complex with the K-26 tripeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L44
- Type
- protein
- Length
- 1,324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K-26 dipeptidyl carboxypeptidase
- Ligands
- K26, MG, ZN, SO4
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | K-26 dipeptidyl carboxypeptidase | protein | 662 | 59% helix, 7% strand | — |
Ligands and binding sites
- K26 · N-acetyl-L-ile-L-tyr-(R)-1-amino-2-(4-hydroxyphenyl)ethylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.89 | 0.90 | 114 | MG, SO4, K26 |
| 2 | 887 | 0.89 | 0.91 | 108 | MG, SO4 |
| 3 | 337 | 0.72 | 0.84 | 44 | empty |
| 4 | 326 | 0.71 | 0.84 | 42 | empty |
| 5 | 289 | 0.65 | 0.82 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 606 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5L44 · Structure of K-26-DCP in complex with the K-26 tripeptide · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5L44 · PDBe 5L44
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