Research workbench
Smallpox virus topoisomerase-DNA transition state
Analyse Smallpox virus topoisomerase-DNA transition state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IGC
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 1; 5'-D(*GP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'; 5'-D(*AP*TP*TP*CP*C)-3'…
- EC
- 5.99.1.2
- UniProt
- P32989
- Ligands
- VO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 1 (EC 5.99.1.2) | protein | 313 | 52% helix, 14% strand | P32989 |
| B | 5'-D(*GP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3' | dna | 11 | — | — |
| C | 5'-D(*AP*TP*TP*CP*C)-3' | dna | 5 | — | — |
| D | 5'-D(*CP*GP*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3' | dna | 16 | — | — |
Ligands and binding sites
- VO4 · Vanadate ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.74 | 0.81 | 47 | empty |
| 2 | 408 | 0.65 | 0.79 | 51 | empty |
| 3 | 145 | 0.57 | 0.83 | 29 | empty |
| 4 | 110 | 0.40 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–D · 993 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 779 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–D · 479 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–C · 321 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 254 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Compared structures
- 3IGC · Smallpox virus topoisomerase-DNA transition state · 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 P32989
- Elsewhere: RCSB PDB 3IGC · PDBe 3IGC · UniProt P32989
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