MolNFT v1 · #12047 · protein + DNA
Human DNA topoisomerase I (70 kda) in complex with the poison topotecan and covalent complex with a 22 base pair DNA duplex
1K4T · 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3': “Human DNA topoisomerase I (70 kda) in complex with the poison topotecan and covalent complex with a 22 base…”. X-ray diffraction, 3 ligands (TTG, TTC, HG), 8 pockets (best druggability 0.87).…
- PDB
- 1K4T
- 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
- TTG, TTC, HG
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 50% 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 | 50% helix, 12% strand | P11387 |
Ligands and binding sites
- TTG · 2-(1-dimethylaminomethyl-2-hydroxy-8-hydroxymethyl-9-oxo-9,11-dihydro-indolizino[1,2-b]quinolin-7-yl)-2-hydroxy-butyric acid · ligand · chains B, C, D, A
- TTC · (S)-10-[(dimethylamino)methyl]-4-ethyl-4,9-dihydroxy-1H-pyrano[3',4':6,7]inolizino[1,2-B]-quinoline-3, 14(4H,12H)-dione · ligand · chains B, C, D, A
- HG · Mercury (II) ion · metal · chains A
- PG4 · Tetraethylene glycol · additive · chains 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 | 1040 | 0.87 | 0.88 | 102 | TTG, TTC |
| 2 | 302 | 0.66 | 0.82 | 32 | empty |
| 3 | 82 | 0.53 | 0.85 | 19 | empty |
| 4 | 202 | 0.46 | 0.74 | 18 | empty |
| 5 | 72 | 0.42 | 0.80 | 12 | empty |
Interfaces
5 interfaces between chains.
- D–A · 904 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–A · 575 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 536 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–D · 429 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- C–A · 422 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification, phosphorylation).
Compared structures
- 1K4T · Human DNA topoisomerase I (70 kda) in complex with the poison topotecan and covalent… · 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 1K4T · PDBe 1K4T · UniProt P11387
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