1YMM

TCR/HLA-DR2b/MBP-peptide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain191Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR beta chain198Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
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PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MBP peptide23Homo sapiensMutation(s): 0 
Gene Names: MBP
UniProt & NIH Common Fund Data Resources
Find proteins for P02686 (Homo sapiens)
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PHAROS:  P02686
GTEx:  ENSG00000197971 
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UniProt GroupP02686
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha chain207Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor beta chain249Homo sapiensMutation(s): 2 
UniProt
Find proteins for P01850 (Homo sapiens)
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Go to UniProtKB:  P01850
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UniProt GroupP01850
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.34α = 90
b = 212.62β = 90
c = 278.22γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2021-10-20
    Changes: Advisory, Database references, Structure summary