MolNFT v1 · #120287 · protein
Human TOP3B-TDRD3 complex
5GVE · DNA topoisomerase 3-beta-1: “Human TOP3B-TDRD3 complex”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.74). MolNFT v1 #120287 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GVE
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 3-beta-1; Tudor domain-containing protein 3
- EC
- 5.99.1.2
- UniProt
- O95985, Q9H7E2
- Ligands
- MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 3-beta-1 (EC 5.99.1.2) | protein | 611 | 42% helix, 20% strand | O95985 |
| B | Tudor domain-containing protein 3 | protein | 165 | 19% helix, 27% strand | Q9H7E2 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.74 | 0.77 | 120 | MG |
| 2 | 68 | 0.36 | 0.78 | 11 | empty |
| 3 | 60 | 0.33 | 0.77 | 14 | empty |
| 4 | 57 | 0.32 | 0.77 | 13 | empty |
| 5 | 50 | 0.29 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 787 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5GVE · Human TOP3B-TDRD3 complex · the same entry in another collection · chain A against A, TM-score 1.00
- O95985 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 3-beta-1 (O95985) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9H7E2 · AlphaFold monomer V2.0 prediction for tudor domain-containing protein 3 (Q9H7E2) · a predicted model of the same protein · chain B against A, TM-score 0.39
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 O95985
- Every structure of UniProt Q9H7E2
- Elsewhere: RCSB PDB 5GVE · PDBe 5GVE · UniProt O95985 · UniProt Q9H7E2
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