3P4M | pdb_00003p4m

Crystal Structure of H2-Kb in complex with the NP205-LCMV epitope YTVKYPNL, an 8-mer peptide from the LCMV

• PDB DOI: https://doi.org/10.2210/pdb3P4M/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Mammarenavirus choriomeningitidis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-06 Released: 2011-10-12 
• Deposition Author(s): Gras, S., Guillonneau, C., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of H2-Kb in complex with the NP205-LCMV epitope YTVKYPNL, an 8-mer peptide from the LCMV

Gras, S., Guillonneau, C., Rossjohn, J.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.7 kDa 
• Atom Count: 6,637 
• Modeled Residue Count: 769 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A, D	278	Mus musculus	Mutation(s): 0  Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NP205-LCMV epitope, YTVKYPNL	C, F	8	N/A	Mutation(s): 0  EC: 3.1.13
UniProt
Find proteins for Q91B91 (Mammarenavirus choriomeningitidis) Explore Q91B91  Go to UniProtKB:  Q91B91

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACE	G [auth B], H [auth E]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.73	α = 90
b = 90.92	β = 111.09
c = 89.05	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Gras, S., Guillonneau, C., Rossjohn, J.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description