MolNFT v1 · #191372 · protein + DNA
Structure of M. kandleri topoisomerase V in complex with DNA. 39 base pair symmetric DNA complex
8DFB: “Structure of M. kandleri topoisomerase V in complex with DNA. 39 base pair symmetric DNA complex”. X-ray diffraction, 1 ligand (K), 20 pockets (best druggability 0.86). MolNFT v1 #191372 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8DFB
- Type
- protein + DNA
- Length
- 1,780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase V; DNA (40-mer)
- UniProt
- Q977W1
- Ligands
- K
- Pockets
- 20 · best druggability 0.86
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 (40-mer) | dna | 40 | — | — |
| V | DNA (40-mer) | dna | 40 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.86 | 0.88 | 84 | empty |
| 2 | 1200 | 0.85 | 0.86 | 86 | empty |
| 3 | 762 | 0.78 | 0.83 | 61 | empty |
| 4 | 939 | 0.76 | 0.79 | 97 | K |
| 5 | 478 | 0.74 | 0.84 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3957 Ų buried · 78 hydrogen bonds · protein-protein
- U–V · 2255 Ų buried · 159 hydrogen bonds · nucleic-nucleic
- A–V · 1578 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–U · 1545 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–U · 1348 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 8DFB · Structure of M. kandleri topoisomerase V in complex with DNA. 39 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 8DFB · PDBe 8DFB · UniProt Q977W1
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