MolNFT v1 · #92670 · protein
Crystal structure of topo-78, an N-terminal 78KDA fragment of topoisomerase V
4GFJ: “Crystal structure of topo-78, an N-terminal 78KDA fragment of topoisomerase V”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.78). MolNFT v1 #92670 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GFJ
- Type
- protein
- Length
- 610 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase V
- UniProt
- F1SVL0
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Topoisomerase V | protein | 610 | 64% helix, 2% strand | F1SVL0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.78 | 0.83 | 66 | GOL |
| 2 | 173 | 0.59 | 0.82 | 23 | empty |
| 3 | 210 | 0.54 | 0.78 | 31 | empty |
| 4 | 114 | 0.54 | 0.82 | 19 | empty |
| 5 | 75 | 0.31 | 0.74 | 20 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4GFJ · Crystal structure of Topo-78, an N-terminal 78kDa fragment of topoisomerase V · the same entry in another collection · chain A against A, 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
- Every structure of UniProt F1SVL0
- Elsewhere: RCSB PDB 4GFJ · PDBe 4GFJ · UniProt F1SVL0
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