Research workbench
Crystal structure of N-terminal 44 kda fragment of topoisomerase V in the presence of guanidium hydrochloride
Analyse Crystal structure of N-terminal 44 kda fragment of topoisomerase V in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M6K
- Type
- protein
- Length
- 727 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase V
- UniProt
- Q977W1
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Topoisomerase V | protein | 370 | 61% helix, 4% strand | Q977W1 |
| B | Topoisomerase V | protein | 357 | 63% helix, 4% strand | Q977W1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.80 | 0.82 | 88 | PO4 |
| 2 | 615 | 0.78 | 0.84 | 50 | empty |
| 3 | 499 | 0.72 | 0.81 | 57 | empty |
| 4 | 350 | 0.65 | 0.80 | 27 | empty |
| 5 | 242 | 0.60 | 0.80 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3M6K · Crystal Structure of N-terminal 44 kDa fragment of topoisomerase V in the presence of… · 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 Q977W1
- Elsewhere: RCSB PDB 3M6K · PDBe 3M6K · UniProt Q977W1
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