8PKC | pdb_00008pkc

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.10 Å
R-Value Free:
0.296 (Depositor), 0.295 (DCC)
R-Value Work:
0.258 (Depositor), 0.258 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Aagaard, J.B.

To be published.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00630
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

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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	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.10 Å
R-Value Free: 0.296 (Depositor), 0.295 (DCC)
R-Value Work: 0.258 (Depositor), 0.258 (DCC)
R-Value Observed: 0.262 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.