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Crystal structure of the calcium-binding pollen allergen che a 3

Analyse Crystal structure of the calcium-binding pollen allergen che a 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OPO
Type: protein
Length: 329 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polcalcin che a 3
UniProt: Q84V36
Ligands: CA, SO4
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Polcalcin che a 3	protein	81	63% helix, 6% strand	Q84V36
C	Polcalcin che a 3	protein	85	68% helix, 5% strand	Q84V36
D	Polcalcin che a 3	protein	82	67% helix, 5% strand	Q84V36

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains B, A, C

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	375	0.85	0.93	44	empty
2	499	0.84	0.90	49	empty
3	63	0.36	0.78	13	empty
4	64	0.34	0.77	15	empty

Interfaces

5 interfaces between chains.

A–B · 2720 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2711 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 490 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 61 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 49 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2OPO · Crystal structure of the calcium-binding pollen allergen Che a 3 · the same entry in another collection · chain A against A, TM-score 1.00
Q84V36 · AlphaFold monomer V2.0 prediction for polcalcin che a 3 (Q84V36) · a predicted model of the same protein · chain D against A, TM-score 0.51

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 Q84V36
Elsewhere: RCSB PDB 2OPO · PDBe 2OPO · UniProt Q84V36

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