Research workbench
2.42A crystal structure of mycobacterium tuberculosis topoisomerase I in complex with an oligonucleotide MTS2-11
Analyse 2.42A crystal structure of mycobacterium tuberculosis topoisomerase I in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CQI
- Type
- protein + DNA
- Length
- 695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 1; DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3')
- EC
- 5.99.1.2
- UniProt
- P9WG49
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 1 (EC 5.99.1.2) | protein | 685 | 37% helix, 21% strand | P9WG49 |
| B | DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A
- FMT · Formic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.75 | 0.94 | 33 | empty |
| 2 | 409 | 0.67 | 0.80 | 37 | empty |
| 3 | 441 | 0.65 | 0.78 | 45 | empty |
| 4 | 496 | 0.62 | 0.76 | 52 | FMT |
| 5 | 51 | 0.53 | 0.88 | 13 | GOL |
Interfaces
1 interface between chains.
- A–B · 1357 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 6CQI · 2.42A Crystal structure of Mycobacterium tuberculosis Topoisomerase I in complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WG49 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P9WG49) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P9WG49
- Elsewhere: RCSB PDB 6CQI · PDBe 6CQI · UniProt P9WG49
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