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Crystal structure of PD(ALLYL)/WILD type polyhedra

Analyse Crystal structure of PD(ALLYL)/WILD type polyhedra in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YHA
Type: protein
Length: 247 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyhedrin
UniProt: P11041
Ligands: PLL, ACE, PD, CL
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyhedrin	protein	247	25% helix, 29% strand	P11041

Ligands and binding sites

PLL · Palladium(II) allyl complex · ligand · 3 copies · chains A
ACE · Acetyl group · ligand · chains A
PD · Palladium ion · metal · 5 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.53	0.79	22	empty
2	106	0.36	0.74	17	empty
3	63	0.32	0.76	17	empty
4	59	0.29	0.74	19	PLL

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5YHA · Crystal structure of Pd(allyl)/Wild Type 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 5YHA · PDBe 5YHA · UniProt P11041

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