MolNFT v1 · #60860 · protein
Crystal structure of staphylococcal nuclease variant DELTA+PHS Y91E at cryogenic temperature
3D4D · Thermonuclease: “Crystal structure of staphylococcal nuclease variant DELTA+PHS Y91E at cryogenic temperature”. X-ray diffraction, 2 ligands (THP, CA), 3 pockets (best druggability 0.62). MolNFT v1 #60860 on GenesisL1: 3D structure…
- PDB
- 3D4D
- Type
- protein
- Length
- 258 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
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thermonuclease (EC 3.1.31.1) | protein | 129 | 29% helix, 33% 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
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 | 405 | 0.62 | 0.77 | 52 | empty |
| 2 | 79 | 0.43 | 0.80 | 16 | THP |
| 3 | 63 | 0.41 | 0.81 | 14 | THP |
Interfaces
1 interface between chains.
- A–B · 317 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3D4D · Crystal structure of Staphylococcal nuclease variant Delta+PHS Y91E at cryogenic… · 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 3D4D · PDBe 3D4D · UniProt P00644
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.