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), 0.290 (DCC)
R-Value Work:
0.258 (Depositor), 0.260 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00630
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AM1-4 nanobody	C, D	129	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	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), 0.290 (DCC)
R-Value Work: 0.258 (Depositor), 0.260 (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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Ligand Structure Quality Assessment

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

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.