Research workbench
Crystal structure of the endonuclease V (SAV1684) from streptomyces avermitilis. northeast structural genomics consortium target SVR196
Analyse Crystal structure of the endonuclease V (SAV1684) from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GOC
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V
- EC
- 3.1.21.7
- UniProt
- Q82MH6
- Ligands
- YES, MG, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endonuclease V (EC 3.1.21.7) | protein | 228 | 28% helix, 27% strand | Q82MH6 |
Ligands and binding sites
- YES · 3-(2-hydroxyethyl)-2,2-bis(hydroxymethyl)pentane-1,5-diol · ligand · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.70 | 0.80 | 54 | YES |
| 2 | 245 | 0.59 | 0.79 | 30 | MG, CL |
| 3 | 231 | 0.58 | 0.79 | 34 | MG |
| 4 | 60 | 0.55 | 0.89 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3GOC · Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis.… · the same entry in another collection · chain A against A, TM-score 1.00
- Q82MH6 · AlphaFold monomer V2.0 prediction for endonuclease V (Q82MH6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q82MH6
- Elsewhere: RCSB PDB 3GOC · PDBe 3GOC · UniProt Q82MH6
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