Research workbench
Crystal structure of EXD2 exonuclease domain soaked in mn and mg
Analyse Crystal structure of EXD2 exonuclease domain soaked in mn and mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K1A
- Type
- protein
- Length
- 391 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
- MN, MG
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease 3'-5' domain-containing protein 2 (EC 3.1.11.1) | protein | 195 | 47% helix, 13% strand | Q9NVH0 |
| B | Exonuclease 3'-5' domain-containing protein 2 (EC 3.1.11.1) | protein | 196 | 49% helix, 14% strand | Q9NVH0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.55 | 0.86 | 14 | empty |
| 2 | 193 | 0.47 | 0.75 | 21 | MN, MG |
| 3 | 158 | 0.45 | 0.76 | 23 | MG |
Interfaces
1 interface between chains.
- A–B · 4217 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 6K1A · Crystal structure of EXD2 exonuclease domain soaked in Mn and Mg · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NVH0 · AlphaFold monomer V2.0 prediction for exonuclease 3'-5' domain- containing protein 2… · a predicted model of the same protein · chain B against A, TM-score 0.60
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 6K1A · PDBe 6K1A · UniProt Q9NVH0
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