Research workbench
Human exonuclease 5 crystal structure (T88E) in complex with ssdna and mg
Analyse Human exonuclease 5 crystal structure (T88E) in complex with ssdna and mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LWA
- Type
- protein + DNA
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exonuclease V; DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
- EC
- 3.1.-.-
- UniProt
- Q9H790
- Ligands
- SF4, MG
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease V (EC 3.1.-.-) | protein | 258 | 47% helix, 19% strand | Q9H790 |
| B | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 3 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- MG · Magnesium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.49 | 0.75 | 22 | empty |
| 2 | 102 | 0.39 | 0.76 | 15 | empty |
| 3 | 94 | 0.37 | 0.76 | 19 | empty |
| 4 | 67 | 0.33 | 0.76 | 17 | empty |
| 5 | 67 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 356 Ų buried · 7 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 7LWA · PDBe 7LWA · UniProt Q9H790
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