Research workbench
Crystal structure of a complex between H365R mutant of 67 kda N- terminal fragment of E. COLI DNA topoisomerase I and 5'-acttcgggatg- 3'
Analyse Crystal structure of a complex between H365R mutant of 67 kda N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MW8
- Type
- protein + DNA
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*CP*TP*TP*CP*GP*GP*GP*AP*TP*G)-3'; DNA topoisomerase I
- EC
- 5.99.1.2
- UniProt
- P06612
- Ligands
- TMP, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | 5'-D(*AP*CP*TP*TP*CP*GP*GP*GP*AP*TP*G)-3' | dna | 6 | — | — |
| X | DNA topoisomerase I (EC 5.99.1.2) | protein | 561 | 45% helix, 19% strand | P06612 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.65 | 0.84 | 26 | TMP |
| 2 | 99 | 0.64 | 0.89 | 15 | empty |
| 3 | 106 | 0.52 | 0.83 | 24 | empty |
| 4 | 106 | 0.49 | 0.81 | 15 | empty |
| 5 | 70 | 0.44 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- Y–X · 873 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 1MW8 · Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E.… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P06612 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P06612) · a predicted model of the same protein · chain X against A, TM-score 0.97
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 P06612
- Elsewhere: RCSB PDB 1MW8 · PDBe 1MW8 · UniProt P06612
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