MolNFT v1 · #136654 · protein + DNA
Crystal structure of human exonuclease 1 EXO1 (wt) in complex with 5' recessed-end DNA (ri)
5UZV: “Crystal structure of human exonuclease 1 EXO1 (wt) in complex with 5' recessed-end DNA (ri)”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.81). MolNFT v1 #136654 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5UZV
- Type
- protein + DNA
- Length
- 369 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease 1; DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*C)-3'); DNA…
- EC
- 3.1.-.-
- UniProt
- Q9UQ84
- Ligands
- NA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Exonuclease 1 (EC 3.1.-.-) | protein | 348 | 48% helix, 12% strand | Q9UQ84 |
| A | DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*C)-3') | dna | 11 | — | — |
| B | DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3') | dna | 10 | — | — |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.81 | 0.82 | 89 | empty |
| 2 | 192 | 0.47 | 0.76 | 25 | empty |
| 3 | 63 | 0.42 | 0.81 | 18 | empty |
| 4 | 89 | 0.42 | 0.78 | 13 | empty |
| 5 | 74 | 0.31 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 471 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- Z–B · 370 Ų buried · 5 hydrogen bonds · protein-nucleic
- Z–A · 365 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 5UZV · Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA… · the same entry in another collection · chain Z against Z, 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 5UZV · PDBe 5UZV · UniProt Q9UQ84
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