Research workbench
Crystal structure of staphylococcal nuclease variant DELTA+PHS L36K L103K at cryogenic temperature
Analyse Crystal structure of staphylococcal nuclease variant DELTA+PHS L36K L103K at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I9O
- 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
- 4 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Thermonuclease (EC 3.1.31.1) | protein | 129 | 29% helix, 30% strand | P00644 |
Ligands and binding sites
- THP · Thymidine-3',5'-diphosphate · ligand · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.43 | 0.74 | 20 | empty |
| 2 | 88 | 0.42 | 0.79 | 16 | THP |
| 3 | 84 | 0.42 | 0.79 | 18 | THP |
| 4 | 50 | 0.30 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 474 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5I9O · Crystal structure of Staphylococcal nuclease variant Delta+PHS L36K L103K at cryogenic… · the same entry in another collection · chain B against B, 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 5I9O · PDBe 5I9O · UniProt P00644
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