MolNFT v1 · #154135 · protein
Crystal structure of EXD2 exonuclease domain
6K17 · Exonuclease 3'-5' domain-containing protein 2: “Crystal structure of EXD2 exonuclease domain”. X-ray diffraction, 1 ligand (NA), 2 pockets (best druggability 0.42). MolNFT v1 #154135 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6K17
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease 3'-5' domain-containing protein 2
- EC
- 3.1.11.1
- UniProt
- Q9NVH0
- Ligands
- NA
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease 3'-5' domain-containing protein 2 (EC 3.1.11.1) | protein | 200 | 46% helix, 16% strand | Q9NVH0 |
| B | Exonuclease 3'-5' domain-containing protein 2 (EC 3.1.11.1) | protein | 197 | 47% helix, 16% strand | Q9NVH0 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.42 | 0.75 | 30 | NA |
| 2 | 114 | 0.38 | 0.75 | 22 | NA |
Interfaces
1 interface between chains.
- A–B · 4434 Ų buried · 42 hydrogen bonds · protein-protein
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 Q9NVH0
- Elsewhere: RCSB PDB 6K17 · PDBe 6K17 · UniProt Q9NVH0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.