Research workbench
Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (f2I)
Analyse Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V0C
- Type
- protein + DNA
- Length
- 362 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.58
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Exonuclease 1; DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*A)-3'); DNA…
- EC
- 3.1.-.-
- UniProt
- Q9UQ84
- Ligands
- NA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.58 · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Exonuclease 1 (EC 3.1.-.-) | protein | 347 | 48% helix, 12% strand | Q9UQ84 |
| A | DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*A)-3') | dna | 8 | — | — |
| B | DNA (5'-D(P*AP*CP*TP*AP*GP*CP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains Z, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.72 | 0.80 | 50 | empty |
| 2 | 281 | 0.51 | 0.74 | 37 | NA |
| 3 | 174 | 0.45 | 0.75 | 21 | empty |
| 4 | 82 | 0.32 | 0.74 | 17 | empty |
| 5 | 65 | 0.29 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 358 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- Z–A · 215 Ų buried · 8 hydrogen bonds · protein-nucleic
- Z–B · 49 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5V0C · Crystal structure of human exonuclease 1 EXO1 (wt) in complex with 5' flap DNA (F2I) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UQ84 · AlphaFold monomer V2.0 prediction for exonuclease 1 (Q9UQ84) · a predicted model of the same protein · chain Z against A, TM-score 0.98
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 Q9UQ84
- Elsewhere: RCSB PDB 5V0C · PDBe 5V0C · UniProt Q9UQ84
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