MolNFT v1 · #140938 · protein

Crystal structure of oxidized cypovirus polyhedra R13A/S193C/A194C mutant

5YRD · Polyhedrin: “Crystal structure of oxidized cypovirus polyhedra R13A/S193C/A194C mutant”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #140938 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YRD
Type: protein
Length: 241 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyhedrin
UniProt: P11041
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyhedrin	protein	241	24% helix, 32% strand	P11041

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 5 copies · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	154	0.53	0.80	21	EDO
2	56	0.28	0.75	12	empty
3	53	0.27	0.74	10	empty

Compared structures

5YRD · Crystal Structure of Oxidized Cypovirus Polyhedra R13A/S193C/A194C Mutant · 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 5YRD · PDBe 5YRD · UniProt P11041

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