9CX2 | pdb_00009cx2

Crystal structure of HLA-A*03:01 L156Q mutant in complex with a mutant PIK3CA peptide

• PDB DOI: https://doi.org/10.2210/pdb9CX2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-07-30 Released: 2026-02-04 
• Deposition Author(s): Ma, J., Perera, W.W.J.G., Baker, B.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 

Starting Model: experimental

Literature

Crystal structure of HLA-A*03:01 L156Q mutant in complex with a mutant PIK3CA peptide

Ma, J., Perera, W.W.J.G., Baker, B.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.5 kDa 
• Atom Count: 3,435 
• Modeled Residue Count: 383 
• Deposited Residue Count: 383 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	A	274	Homo sapiens	Mutation(s): 1  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mutant PIK3CA peptide	C	9	Homo sapiens	Mutation(s): 1  EC: 2.7.1.137 (UniProt), 2.7.11.1 (UniProt), 2.7.1.153 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336 GTEx:  ENSG00000121879

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.424	α = 90
b = 156.424	β = 90
c = 85.639	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Ma, J., Perera, W.W.J.G., Baker, B.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118166

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release