Research workbench
Crystal structure of the exonuclease domain of qip (qde-2 interacting protein) solved by native-sad phasing.
Analyse Crystal structure of the exonuclease domain of qip (qde-2 interacting protein)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WBQ
- Type
- protein
- Length
- 347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Qde-2-interacting protein
- UniProt
- A5JQJ3
- Ligands
- CA
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Qde-2-interacting protein | protein | 174 | 48% helix, 26% strand | A5JQJ3 |
| B | Qde-2-interacting protein | protein | 173 | 46% helix, 28% strand | A5JQJ3 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.57 | 0.87 | 26 | empty |
| 2 | 202 | 0.49 | 0.76 | 30 | CA |
| 3 | 77 | 0.34 | 0.76 | 17 | CA |
| 4 | 55 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2874 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4WBQ · Crystal structure of the exonuclease domain of QIP (QDE-2 interacting protein) solved by… · 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 A5JQJ3
- Elsewhere: RCSB PDB 4WBQ · PDBe 4WBQ · UniProt A5JQJ3
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