Research workbench
Crystal structure of a repair endonuclease from pyrococcus abyssi
Analyse Crystal structure of a repair endonuclease from pyrococcus abyssi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VLD
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease nucs
- EC
- 3.1.-.-
- UniProt
- Q9V2E8
- Pockets
- 8 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease nucs (EC 3.1.-.-) | protein | 228 | 24% helix, 43% strand | Q9V2E8 |
| B | Endonuclease nucs (EC 3.1.-.-) | protein | 226 | 24% helix, 44% strand | Q9V2E8 |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.49 | 0.80 | 21 | empty |
| 2 | 117 | 0.49 | 0.80 | 21 | empty |
| 3 | 111 | 0.48 | 0.80 | 18 | empty |
| 4 | 115 | 0.47 | 0.79 | 19 | empty |
| 5 | 84 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3001 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
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 Q9V2E8
- Elsewhere: RCSB PDB 2VLD · PDBe 2VLD · UniProt Q9V2E8
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