MolNFT v1 · #21492 · protein + DNA
Human DNA topoisomerase I (70 kda) in complex with the indenoisoquinoline mj-II-38 and covalent complex with a 22 base pair DNA duplex
1SC7 · 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3': “Human DNA topoisomerase I (70 kda) in complex with the indenoisoquinoline mj-II-38 and covalent complex with…”. X-ray diffraction, 1 ligand (M38), 12 pockets (best druggability 0.84). MolNFT…
- PDB
- 1SC7
- Type
- protein + DNA
- Length
- 611 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
- M38
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 11% 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 | 567 | 43% helix, 11% strand | P11387 |
Ligands and binding sites
- M38 · 4-(5,11-dioxo-5H-indeno[1,2-c]isoquinolin-6(11H)-yl)butanoate · ligand · chains B, C, D, A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.84 | 0.88 | 85 | M38 |
| 2 | 554 | 0.69 | 0.79 | 41 | empty |
| 3 | 199 | 0.68 | 0.86 | 28 | empty |
| 4 | 190 | 0.60 | 0.82 | 25 | empty |
| 5 | 92 | 0.49 | 0.82 | 14 | empty |
Interfaces
5 interfaces between chains.
- D–A · 846 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–A · 627 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 537 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- C–A · 485 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 429 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification, phosphorylation).
Compared structures
- 1SC7 · Human DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoquinoline MJ-II-38 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 0.98
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 1SC7 · PDBe 1SC7 · UniProt P11387
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.