Research workbench
Crystal structure of staphylococcal nuclease variant DELTA+PHS K64G/V66K/E67G at cryogenic temperature
Analyse Crystal structure of staphylococcal nuclease variant DELTA+PHS K64G/V66K/E67G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CV5
- Type
- protein
- Length
- 254 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 0.54
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermonuclease (EC 3.1.31.1) | protein | 129 | 28% helix, 32% strand | P00644 |
| B | Thermonuclease (EC 3.1.31.1) | protein | 125 | 26% helix, 31% 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.54 | 0.77 | 31 | empty |
| 2 | 88 | 0.42 | 0.79 | 18 | THP |
| 3 | 67 | 0.40 | 0.80 | 14 | THP |
| 4 | 74 | 0.38 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 438 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5CV5 · Crystal structure of Staphylococcal nuclease variant Delta+PHS K64G/V66K/E67G at… · 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 5CV5 · PDBe 5CV5 · UniProt P00644
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