MolNFT v1 · #87974 · protein
Crystal structure of the human topoisomerase III alpha-RMI1 complex
4CGY · DNA topoisomerase 3-alpha: “Crystal structure of the human topoisomerase III alpha-RMI1 complex”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.62). MolNFT v1 #87974 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4CGY
- Type
- protein
- Length
- 824 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 3-alpha; Recq-mediated genome instability protein 1
- EC
- 5.99.1.2
- UniProt
- Q13472, Q9H9A7
- Ligands
- MG
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 3-alpha (EC 5.99.1.2) | protein | 619 | 45% helix, 19% strand | Q13472 |
| B | Recq-mediated genome instability protein 1 | protein | 205 | 36% helix, 21% strand | Q9H9A7 |
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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.62 | 0.78 | 40 | empty |
| 2 | 477 | 0.61 | 0.76 | 58 | MG |
| 3 | 231 | 0.47 | 0.74 | 29 | empty |
| 4 | 164 | 0.44 | 0.75 | 27 | empty |
| 5 | 59 | 0.44 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1401 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4CGY · Crystal structure of the human topoisomerase III alpha-RMI1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q13472 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 3-alpha (Q13472) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q9H9A7 · AlphaFold monomer V2.0 prediction for recq-mediated genome instability protein 1 (Q9H9A7) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q13472
- Every structure of UniProt Q9H9A7
- Elsewhere: RCSB PDB 4CGY · PDBe 4CGY · UniProt Q13472 · UniProt Q9H9A7
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