MolNFT v1 · #140721 · protein

Structure of vicilin from capsicum annuum

5YJS · Vicilin-like antimicrobial peptides 2-2: “Structure of vicilin from capsicum annuum”. X-ray diffraction, 4 ligands (SAL, CU1, NA), 6 pockets (best druggability 0.72). MolNFT v1 #140721 on GenesisL1: 3D structure, binding sites and…

PDB: 5YJS
Type: protein
Length: 740 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vicilin-like antimicrobial peptides 2-2
Ligands: SAL, CU1, NA, CL
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vicilin-like antimicrobial peptides 2-2	protein	370	18% helix, 39% strand	—

Ligands and binding sites

SAL · 2-hydroxybenzoic acid · ligand · 2 copies · chains A, B
CU1 · Copper (I) ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · chains A
PG4 · Tetraethylene glycol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	511	0.72	0.81	73	empty
2	715	0.67	0.75	69	empty
3	115	0.65	0.88	26	empty
4	126	0.62	0.86	28	PG4
5	94	0.37	0.75	28	empty

Interfaces

1 interface between chains.

A–B · 604 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5YJS · Structure of vicilin from Capsicum annuum · 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
Elsewhere: RCSB PDB 5YJS · PDBe 5YJS

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