Research workbench
Human exonuclease 5 crystal structure in complex with a ssdna
Analyse Human exonuclease 5 crystal structure in complex with a ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LW8
- Type
- protein + DNA
- Length
- 269 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
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exonuclease V (EC 3.1.-.-) | protein | 260 | 45% helix, 18% strand | Q9H790 |
| B | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- IMD · Imidazole · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.62 | 0.79 | 27 | empty |
| 2 | 135 | 0.42 | 0.76 | 22 | empty |
| 3 | 70 | 0.35 | 0.76 | 12 | empty |
| 4 | 84 | 0.33 | 0.75 | 16 | EDO |
| 5 | 56 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1108 Ų buried · 30 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 7LW8 · PDBe 7LW8 · UniProt Q9H790
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