8PKC

Structure of Api m1 in complex with the AM1-4 nanobody

• PDB DOI: https://doi.org/10.2210/pdb8PKC/pdb

• Classification: ALLERGEN
• Organism(s): Apis mellifera, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-26 Released: 2024-05-08 
• Deposition Author(s): Aagaard, J.B., Gandini, R., Spillner, E., Miehe, M.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.296 
• R-Value Work: 0.258 
• R-Value Observed: 0.262 

Starting Model: experimental

Literature

Nanobody-based IgG formats as blocking antibodies of the major honeybee venom allergen Api m 1

Aagaard, J.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.58 kDa 
• Atom Count: 4,065 
• Modelled Residue Count: 522 
• Deposited Residue Count: 526 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A, B	134	Apis mellifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P00630 (Apis mellifera) Explore P00630  Go to UniProtKB:  P00630
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AM1-4 nanobody	C, D	129	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.296 
• R-Value Work: 0.258 
• R-Value Observed: 0.262 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.6	α = 90
b = 93.6	β = 90
c = 189.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Aagaard, J.B., Gandini, R., Spillner, E., Miehe, M.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	0135-00061B

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release