MolNFT v1 · #12046 · protein + DNA
Human DNA topoisomerase I in covalent complex with a 22 base pair DNA duplex
1K4S · 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*(5IU)P*(5IU))-3': “Human DNA topoisomerase I in covalent complex with a 22 base pair DNA duplex”. X-ray diffraction, 7 pockets (best druggability 0.86). MolNFT v1 #12046 on GenesisL1: 3D structure…
- PDB
- 1K4S
- Type
- protein + DNA
- Length
- 534 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*(5IU)P*(5IU))-3'…
- EC
- 5.99.1.2
- UniProt
- P11387
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*(5IU)P*(5IU))-3' | dna | 10 | — | — |
| C | 5'-D(*(SPT)P*GP*AP*AP*AP*AP*AP*(5IU)P*(5IU) P*(5IU)P*(5IU)P*T)-3' | dna | 12 | — | — |
| D | 5'-D(*AP*AP*AP*AP*AP*TP*(IDO)UP*(IDO)UP*(IDO) UP*(IDO)UP*CP*AP*AP*AP*GP*(IDO)UP*CP*(IDO)UP*(IDO)UP*(IDO) UP*(IDO)UP*T)-3' | dna | 22 | — | — |
| A | DNA topoisomerase I (EC 5.99.1.2) | protein | 490 | 42% helix, 10% strand | P11387 |
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 | 924 | 0.86 | 0.88 | 90 | empty |
| 2 | 140 | 0.72 | 0.91 | 31 | empty |
| 3 | 326 | 0.67 | 0.82 | 39 | empty |
| 4 | 69 | 0.40 | 0.79 | 14 | empty |
| 5 | 64 | 0.39 | 0.80 | 14 | empty |
Interfaces
6 interfaces between chains.
- D–A · 990 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–A · 589 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 505 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- B–D · 434 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- C–A · 332 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 17 modified (nucleotide modification, phosphorylation).
Compared structures
- 1K4S · Human DNA topoisomerase I in 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 0.99
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 1K4S · PDBe 1K4S · UniProt P11387
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