MolNFT v1 · #22549 · protein + DNA
Human DNA topoisomerase I (70 kda) in complex with the poison camptothecin and covalent complex with a 22 base pair DNA duplex
1T8I · 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3': “Human DNA topoisomerase I (70 kda) in complex with the poison camptothecin and covalent complex with a 22…”. X-ray diffraction, 1 ligand (EHD), 8 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 1T8I
- 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
- EHD
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 47% 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 | 47% helix, 12% strand | P11387 |
Ligands and binding sites
- EHD · 4-ethyl-4-hydroxy-1,12-dihydro-4H-2-oxa-6,12A-diaza-dibenzo[b,h]fluorene-3,13-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 | 1004 | 0.87 | 0.88 | 101 | EHD |
| 2 | 308 | 0.66 | 0.82 | 33 | empty |
| 3 | 142 | 0.61 | 0.85 | 30 | empty |
| 4 | 89 | 0.43 | 0.79 | 14 | empty |
| 5 | 75 | 0.38 | 0.78 | 16 | empty |
Interfaces
5 interfaces between chains.
- D–A · 983 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–A · 561 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 559 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- C–A · 468 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 431 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification, phosphorylation).
Compared structures
- 1T8I · Human DNA Topoisomerase I (70 Kda) In Complex With The Poison Camptothecin 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 1T8I · PDBe 1T8I · UniProt P11387
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