MolNFT v1 · #136664 · protein + DNA
Crystal structure of human exonuclease 1 EXO1 (wt) in complex with 5' recessed-end DNA (riii)
5V05: “Crystal structure of human exonuclease 1 EXO1 (wt) in complex with 5' recessed-end DNA (riii)”. X-ray diffraction, 2 ligands (MN, NA), 6 pockets (best druggability 0.77). MolNFT v1 #136664 on GenesisL1: 3D structure, binding sites…
- PDB
- 5V05
- 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*CP*AP*T)-3'); DNA…
- EC
- 3.1.-.-
- UniProt
- Q9UQ84
- Ligands
- MN, NA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Exonuclease 1 (EC 3.1.-.-) | protein | 346 | 49% helix, 13% strand | Q9UQ84 |
| A | DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3') | dna | 13 | — | — |
| B | DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.77 | 0.85 | 52 | MN |
| 2 | 821 | 0.71 | 0.77 | 42 | empty |
| 3 | 61 | 0.51 | 0.86 | 14 | empty |
| 4 | 63 | 0.36 | 0.78 | 14 | empty |
| 5 | 67 | 0.30 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- Z–A · 681 Ų buried · 16 hydrogen bonds · protein-nucleic
- Z–B · 482 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–B · 467 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Compared structures
- 5V05 · 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 0.99
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 5V05 · PDBe 5V05 · UniProt Q9UQ84
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