Research workbench
Crystal structure of staphylococcal nuclease variant V23M at cryogenic temperature
Analyse Crystal structure of staphylococcal nuclease variant V23M at cryogenic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QF4
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermonuclease
- EC
- 3.1.31.1
- UniProt
- P00644
- Ligands
- THP, CA, PO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thermonuclease (EC 3.1.31.1) | protein | 132 | 27% helix, 30% strand | P00644 |
Ligands and binding sites
- THP · Thymidine-3',5'-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.55 | 0.77 | 32 | THP |
| 2 | 133 | 0.45 | 0.77 | 28 | THP, CA |
| 3 | 63 | 0.32 | 0.76 | 11 | PO4 |
Interfaces
1 interface between chains.
- A–B · 300 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4QF4 · Crystal structure of Staphylococcal nuclease variant V23M at cryogenic temperature · 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 P00644
- Elsewhere: RCSB PDB 4QF4 · PDBe 4QF4 · UniProt P00644
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