Research workbench
Human DNA topoisomerase I (70 kda) in non-covalent complex with a 22 base pair DNA duplex containing an 8-oxog lesion
Analyse Human DNA topoisomerase I (70 kda) in non-covalent complex with a 22 base pair… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LPQ
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*(8OG) P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'…
- EC
- 5.99.1.2
- UniProt
- P11387
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*(8OG) P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' | dna | 22 | — | — |
| C | 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP *TP*TP*TP*T)-3' | dna | 22 | — | — |
| A | DNA topoisomerase I (EC 5.99.1.2) | protein | 557 | 41% helix, 11% strand | P11387 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.87 | 0.88 | 101 | empty |
| 2 | 71 | 0.71 | 0.96 | 21 | empty |
| 3 | 388 | 0.69 | 0.81 | 24 | empty |
| 4 | 152 | 0.55 | 0.81 | 22 | empty |
| 5 | 99 | 0.47 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1022 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–A · 980 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 916 Ų buried · 70 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1LPQ · Human DNA Topoisomerase I (70 Kda) In Non-Covalent Complex With A 22 Base Pair DNA Duplex… · the same entry in another collection · chain B against B, TM-score 1.00
- P11387 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P11387) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P11387
- Elsewhere: RCSB PDB 1LPQ · PDBe 1LPQ · UniProt P11387
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