MolNFT v1 · #191370 · protein + DNA
Structure of M. kandleri topoisomerase V in complex with DNA. 40 base pair symmetric DNA complex
8DF8: “Structure of M. kandleri topoisomerase V in complex with DNA. 40 base pair symmetric DNA complex”. X-ray diffraction, 3 ligands (K, PO4, PO3), 20 pockets (best druggability 0.85). MolNFT v1 #191370 on GenesisL1: 3D structure…
- PDB
- 8DF8
- Type
- protein + DNA
- Length
- 1,777 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase V; DNA (42-mer)
- UniProt
- Q977W1
- Ligands
- K, PO4, PO3
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Topoisomerase V | protein | 850 | 66% helix, 2% strand | Q977W1 |
| U | DNA (42-mer) | dna | 39 | — | — |
| V | DNA (42-mer) | dna | 38 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains B, V, A, U
- PO3 · Phosphite ion · ion · 2 copies · chains B, U, A, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.85 | 0.87 | 79 | empty |
| 2 | 964 | 0.85 | 0.87 | 85 | PO4 |
| 3 | 939 | 0.82 | 0.84 | 84 | empty |
| 4 | 261 | 0.82 | 0.94 | 34 | empty |
| 5 | 123 | 0.77 | 0.96 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4141 Ų buried · 74 hydrogen bonds · protein-protein
- U–V · 2104 Ų buried · 137 hydrogen bonds · nucleic-nucleic
- A–V · 1410 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–U · 1233 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–U · 1111 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 8DF8 · Structure of M. kandleri topoisomerase V in complex with DNA. 40 base pair symmetric DNA… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q977W1
- Elsewhere: RCSB PDB 8DF8 · PDBe 8DF8 · UniProt Q977W1
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