Research workbench
Human DNA topoisomerase I (70 kda) in complex with the indolocarbazole SA315F and covalent complex with a 22 base pair DNA duplex
Analyse Human DNA topoisomerase I (70 kda) in complex with the indolocarbazole SA315F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SEU
- Type
- protein + DNA
- Length
- 609 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'; 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'…
- EC
- 5.99.1.2
- UniProt
- P11387
- Ligands
- SA3
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' | dna | 10 | — | — |
| C | 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' | dna | 12 | — | — |
| D | 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 | 565 | 41% helix, 12% strand | P11387 |
Ligands and binding sites
- SA3 · 2,10-dihydroxy-12-(beta-D-glucopyranosyl)-6,7,12,13-tetrahydroindolo[2,3-a]pyrrolo[3,4-c]carbazole-5,7-dione · ligand · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.86 | 0.87 | 95 | SA3 |
| 2 | 556 | 0.69 | 0.79 | 41 | empty |
| 3 | 223 | 0.68 | 0.85 | 27 | empty |
| 4 | 69 | 0.45 | 0.82 | 15 | empty |
| 5 | 88 | 0.35 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- D–A · 1007 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–A · 575 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 538 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- B–D · 430 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- C–A · 423 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification, phosphorylation).
Compared structures
- 1SEU · Human DNA Topoisomerase I (70 Kda) In Complex With The Indolocarbazole SA315F and… · 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 0.99
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 1SEU · PDBe 1SEU · UniProt P11387
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