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Crystal structure of fire ant venom allergen, sol I 2

Analyse Crystal structure of fire ant venom allergen, sol I 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YGU
Type: protein
Length: 943 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Venom allergen 2
UniProt: P35775
Ligands: HP6
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Venom allergen 2	protein	117	69% helix, 0% strand	P35775
B, F	Venom allergen 2	protein	119	66% helix, 0% strand	P35775
C, E, G	Venom allergen 2	protein	118	69% helix, 0% strand	P35775
H	Venom allergen 2	protein	117	71% helix, 0% strand	P35775

Ligands and binding sites

HP6 · Heptane · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.81	0.98	23	HP6
2	115	0.81	0.98	21	HP6
3	118	0.81	0.98	20	HP6
4	113	0.80	0.98	21	HP6
5	116	0.80	0.98	22	HP6

Interfaces

4 interfaces between chains.

A–B · 1179 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1174 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1165 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1125 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

2YGU · Crystal structure of fire ant venom allergen, Sol I 2 · the same entry in another collection · chain H against H, TM-score 1.00
P35775 · AlphaFold monomer V2.0 prediction for venom allergen 2 (P35775) · a predicted model of the same protein · 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 P35775
Elsewhere: RCSB PDB 2YGU · PDBe 2YGU · UniProt P35775

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