MolNFT v1 · #120130 · protein
Crystal structure of wild type cypovirus polyhedra
5GQL · Polyhedrin: “Crystal structure of wild type cypovirus polyhedra”. X-ray diffraction, 5 ligands (ACE, CTP, ATP), 4 pockets (best druggability 0.52). MolNFT v1 #120130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GQL
- Type
- protein
- Length
- 247 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyhedrin
- UniProt
- P11041
- Ligands
- ACE, CTP, ATP, MG, CL
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyhedrin | protein | 247 | 24% helix, 31% strand | P11041 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- CTP · Cytidine-5'-triphosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 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 | 153 | 0.52 | 0.79 | 24 | empty |
| 2 | 65 | 0.32 | 0.76 | 20 | empty |
| 3 | 51 | 0.28 | 0.75 | 10 | empty |
| 4 | 50 | 0.27 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5GQL · Crystal structure of Wild Type Cypovirus Polyhedra · 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 5GQL · PDBe 5GQL · UniProt P11041
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