Research workbench
Crystal structure of EXD2 exonuclease domain soaked in mn and gmp
Analyse Crystal structure of EXD2 exonuclease domain soaked in mn and gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K1D
- Type
- protein
- Length
- 385 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
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 46% 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 | 192 | 46% helix, 15% strand | Q9NVH0 |
| B | Exonuclease 3'-5' domain-containing protein 2 (EC 3.1.11.1) | protein | 193 | 47% helix, 14% strand | Q9NVH0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.70 | 0.97 | 16 | empty |
| 2 | 229 | 0.50 | 0.75 | 27 | MN |
| 3 | 88 | 0.45 | 0.80 | 18 | empty |
| 4 | 151 | 0.43 | 0.75 | 19 | MN |
| 5 | 55 | 0.43 | 0.83 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 4096 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6K1D · Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP · 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 0.61
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 6K1D · PDBe 6K1D · UniProt Q9NVH0
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