Research workbench
Crystal structure of cypovirus polyhedra mutant with deletion of SER193 and ALA194
Analyse Crystal structure of cypovirus polyhedra mutant with deletion of SER193 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GQJ
- Type
- protein
- Length
- 244 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyhedrin
- UniProt
- P11041
- Ligands
- ACE, ATP, CTP, MG, CL
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyhedrin | protein | 244 | 25% helix, 31% strand | P11041 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- CTP · Cytidine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.50 | 0.79 | 22 | EDO |
| 2 | 58 | 0.31 | 0.76 | 11 | empty |
| 3 | 56 | 0.30 | 0.75 | 19 | empty |
| 4 | 53 | 0.28 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5GQJ · Crystal structure of Cypovirus Polyhedra mutant with deletion of Ser193 and Ala194 · 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 P11041
- Elsewhere: RCSB PDB 5GQJ · PDBe 5GQJ · UniProt P11041
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