9GMU | pdb_00009gmu

Structure ofhuman aM ligand binding domain in complex with the aCR3 nanobody

• PDB DOI: https://doi.org/10.2210/pdb9GMU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-29 Released: 2025-09-10 
• Deposition Author(s): Lorentzen, J., Andersen, G.R.
• Funding Organization(s): Lundbeckfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Structure of ligand bound aMb2

Lorentzen, J., Andersen, G.R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.11 kDa 
• Atom Count: 4,874 
• Modeled Residue Count: 612 
• Deposited Residue Count: 656 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-M	A, B	198	Homo sapiens	Mutation(s): 0  Gene Names: ITGAM, CD11B, CR3A
UniProt & NIH Common Fund Data Resources
Find proteins for P11215 (Homo sapiens) Explore P11215  Go to UniProtKB:  P11215
PHAROS:  P11215 GTEx:  ENSG00000169896

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
aCR VHH	C, D	130	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth C], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.564	α = 90
b = 56.142	β = 128.61
c = 137.444	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Lorentzen, J., Andersen, G.R.

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Funding Organization	Location	Grant Number
Lundbeckfonden	Denmark	--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release