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Crystal structure of the major carrot allergen dau C 1

Analyse Crystal structure of the major carrot allergen dau C 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WQL
Type: protein
Length: 608 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major allergen dau C 1
UniProt: O04298
Ligands: CL
Pockets: 4 · best druggability 0.91

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Major allergen dau C 1	protein	152	30% helix, 39% strand	O04298

Ligands and binding sites

CL · Chloride ion · ion · 16 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D
P4C · O-acetaldehydyl-hexaethylene glycol · additive · 4 copies · chains A, B, C, D

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	989	0.91	0.93	115	P4C, PEG
2	925	0.91	0.93	112	P4C, PEG
3	251	0.49	0.74	28	empty
4	244	0.48	0.73	29	empty

Interfaces

3 interfaces between chains.

A–B · 760 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 750 Å² buried · 1 hydrogen bond · protein-protein
A–C · 318 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2WQL · Crystal structure of the major carrot allergen dau C 1 · the same entry in another collection · chain D against D, TM-score 1.00
O04298 · AlphaFold monomer V2.0 prediction for major allergen dau C 1 (O04298) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O04298
Elsewhere: RCSB PDB 2WQL · PDBe 2WQL · UniProt O04298

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