MolNFT v1 · #160169 · protein + DNA
Crystal structure of mycobacterium smegmatis topoisomerase I with ssdna bound to both N- and C-terminal domains
6PCM · DNA topoisomerase 1: “Crystal structure of mycobacterium smegmatis topoisomerase I with ssdna bound to both N- and C-terminal…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.80). MolNFT v1 #160169 on GenesisL1…
- PDB
- 6PCM
- Type
- protein + DNA
- Length
- 1,624 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 1; DNA (5'- D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP…
- EC
- 5.6.2.2
- UniProt
- A0R5D9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 1 (EC 5.6.2.2) | protein | 793 | 34% helix, 21% strand | A0R5D9 |
| B | DNA topoisomerase 1 (EC 5.6.2.2) | protein | 783 | 35% helix, 21% strand | A0R5D9 |
| C, D | DNA (5'- D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP *TP*T)-3') | dna | 24 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 22 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.80 | 0.82 | 116 | empty |
| 2 | 554 | 0.77 | 0.84 | 73 | empty |
| 3 | 1038 | 0.76 | 0.78 | 107 | empty |
| 4 | 62 | 0.65 | 0.94 | 24 | empty |
| 5 | 50 | 0.59 | 0.91 | 12 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1375 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–C · 1333 Ų buried · 37 hydrogen bonds · protein-nucleic
- B–C · 872 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 801 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–D · 705 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PCM · Crystal Structure of Mycobacterium smegmatis Topoisomerase I with ssDNA bound to both N… · the same entry in another collection · chain A against A, TM-score 1.00
- A0R5D9 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (A0R5D9) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 A0R5D9
- Elsewhere: RCSB PDB 6PCM · PDBe 6PCM · UniProt A0R5D9
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