9HML | pdb_00009hml

KIR2DL1 bound to RIFIN PfKE01_040007400

• PDB DOI: https://doi.org/10.2210/pdb9HML/pdb

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


• Deposited: 2024-12-09 Released: 2025-04-09 
• Deposition Author(s): Chamberlain, S.G., Higgins, M.K.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.232 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

RIFINs displayed on malaria-infected erythrocytes bind both KIR2DL1 and KIR2DS1

Chamberlain, S.G., Higgins, M.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 51.61 kDa 
• Atom Count: 3,380 
• Modelled Residue Count: 414 
• Deposited Residue Count: 470 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIFIN PfKE01_040007400	A	140	Plasmodium falciparum	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KIR2DL protein	B	204	Homo sapiens	Mutation(s): 0  Gene Names: KIR2DL1, 3DL2
UniProt
Find proteins for A0A191URJ7 (Homo sapiens) Explore A0A191URJ7  Go to UniProtKB:  A0A191URJ7
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: A0A191URJ7-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody Nb1	C	126	Escherichia coli	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [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: 2.17 Å
• R-Value Free:  0.232 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.171	α = 90
b = 97.171	β = 90
c = 109.202	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Chamberlain, S.G., Higgins, M.K.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	224343/Z/21/Z

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release