MolNFT v1 · #31893 · protein + DNA
Crystal structure of heterodimeric L. donovani topoisomerase I- vanadate-DNA complex
2B9S · 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3': “Crystal structure of heterodimeric L. donovani topoisomerase I- vanadate-DNA complex”. X-ray diffraction, 1 ligand (VO4), 6 pockets (best druggability 0.85). MolNFT v1 #31893 on GenesisL1: 3D…
- PDB
- 2B9S
- Type
- protein + DNA
- Length
- 522 residues
- Chains
- 5
- 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(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'…
- EC
- 5.99.1.2
- Ligands
- VO4
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' | dna | 10 | — | — |
| D | 5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' | dna | 12 | — | — |
| E | 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP *TP*TP*TP*T)-3' | dna | 22 | — | — |
| A | Topoisomerase I-like protein (EC 5.99.1.2) | protein | 426 | 41% helix, 14% strand | — |
| B | DNA topoisomerase I-like protein (EC 5.99.1.2) | protein | 52 | 48% helix, 4% strand | — |
Ligands and binding sites
- VO4 · Vanadate ion · ion · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.85 | 0.87 | 110 | empty |
| 2 | 373 | 0.68 | 0.81 | 37 | empty |
| 3 | 54 | 0.66 | 0.96 | 24 | empty |
| 4 | 100 | 0.44 | 0.79 | 14 | empty |
| 5 | 55 | 0.35 | 0.79 | 14 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1636 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 800 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–A · 576 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–E · 553 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–E · 446 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 2B9S · Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2B9S · PDBe 2B9S
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