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Structure of M. kandleri topoisomerase V in complex with DNA. 38 base pair asymmetric DNA complex
Analyse Structure of M. kandleri topoisomerase V in complex with DNA. 38 base pair… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DF9
- Type
- protein + DNA
- Length
- 1,766 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase V; DNA (33-mer); DNA (5'- D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*G…
- UniProt
- Q977W1
- Ligands
- MG, K
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Topoisomerase V | protein | 781 | 65% helix, 2% strand | Q977W1 |
| B | Topoisomerase V | protein | 845 | 65% helix, 1% strand | Q977W1 |
| S | DNA (33-mer) | dna | 33 | — | — |
| T | DNA (33-mer) | dna | 33 | — | — |
| U | DNA (5'- D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*C)-3') | dna | 17 | — | — |
| V | DNA (5'- D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3') | dna | 20 | — | — |
| W | DNA (5'- D(P*GP*CP*CP*TP*GP*CP*AP*CP*GP*AP*AP*GP*TP*AP*AP*GP*CP*A)-3') | dna | 18 | — | — |
| X | DNA (5'- D(P*TP*GP*CP*TP*TP*AP*CP*TP*TP*CP*GP*TP*GP*CP*AP*GP*GP*CP*CP*A)-3') | dna | 19 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, B, S, T
- K · Potassium ion · metal · 2 copies · chains S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.86 | 0.87 | 102 | empty |
| 2 | 1025 | 0.80 | 0.82 | 71 | empty |
| 3 | 1165 | 0.78 | 0.80 | 73 | empty |
| 4 | 788 | 0.74 | 0.79 | 48 | empty |
| 5 | 776 | 0.73 | 0.78 | 67 | empty |
Interfaces
11 interfaces between chains.
- S–T · 1565 Ų buried · 140 hydrogen bonds · nucleic-nucleic
- A–B · 1496 Ų buried · 24 hydrogen bonds · protein-protein
- W–X · 849 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- U–V · 833 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- B–W · 745 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 8DF9 · Structure of M. kandleri topoisomerase V in complex with DNA. 38 base pair asymmetric DNA… · the same entry in another collection · chain X against X, 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 8DF9 · PDBe 8DF9 · UniProt Q977W1
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