Research workbench
Human exonuclease 5 crystal structure in complex with ssdna, sm, and na
Analyse Human exonuclease 5 crystal structure in complex with ssdna, sm, and na in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LW9
- Type
- protein + DNA
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease V; DNA (5'-D(*AP*TP*TP*GP*CP*TP*GP*AP*AP*GP*GP*G)-3')
- EC
- 3.1.-.-
- UniProt
- Q9H790
- Ligands
- SF4, SM, NA
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease V (EC 3.1.-.-) | protein | 263 | 46% helix, 19% strand | Q9H790 |
| B | DNA (5'-D(*AP*TP*TP*GP*CP*TP*GP*AP*AP*GP*GP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- SM · Samarium (III) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
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 | 67 | 0.68 | 0.94 | 15 | SF4 |
| 2 | 196 | 0.58 | 0.81 | 25 | ACT |
| 3 | 244 | 0.55 | 0.78 | 32 | ACT, NA |
| 4 | 86 | 0.35 | 0.75 | 13 | empty |
| 5 | 73 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
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 Q9H790
- Elsewhere: RCSB PDB 7LW9 · PDBe 7LW9 · UniProt Q9H790
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