MolNFT v1 · #139477 · protein
Crystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q mutant complexed with beta-isoaspartyl lysine
5XGX: “Crystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q mutant complexed with…”. X-ray diffraction, 3 ligands (DAS, DLY, ZN), 3 pockets (best druggability 0.69). MolNFT v1 #139477 on GenesisL1: 3D…
- PDB
- 5XGX
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoaspartyl dipeptidase
- EC
- 3.4.19.-
- UniProt
- Q484B6
- Ligands
- DAS, DLY, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 381 | 29% helix, 29% strand | Q484B6 |
Ligands and binding sites
- DAS · D-aspartic acid · ligand · 2 copies · chains A, B
- DLY · D-lysine · ligand · 2 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.69 | 0.74 | 70 | empty |
| 2 | 164 | 0.66 | 0.87 | 34 | ZN, DAS, DLY |
| 3 | 100 | 0.66 | 0.91 | 29 | ZN, DAS, DLY |
Interfaces
1 interface between chains.
- A–B · 1337 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5XGX · Crystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q… · 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
- Every structure of UniProt Q484B6
- Elsewhere: RCSB PDB 5XGX · PDBe 5XGX · UniProt Q484B6
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