1LK2

1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide

Structural Biology Knowledgebase: 1LK2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.149

Literature

Macromolecules
Sequence Display for 1LK2

Classification: IMMUNE SYSTEM

Total Structure Weight: 45325.12

Macromolecule Entities
Molecule Chains Length Organism Details
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN A 274 Mus musculus Fragment: EXTRACELLULAR DOMAIN, SEQUENCE DATABASE RESIDUES 22-295, NUMBERED 1-274
Gene Name(s): H2-K1 H2-K
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2-microglobulin B 99 Mus musculus Fragment: SEQUENCE DATABASE RESIDUES 21-119, NUMBERED 1-99
Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
INSULIN RECEPTOR, BETA-SUBUNIT P 8 Mus musculus EC#: 2.7.10.1 IUBMB
Fragment: sequence database residues 423-430, numbered 1-8
Gene Name(s): Insr
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A, B (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

B (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.149
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 135.55 α = 90.00
b = 87.65 β = 90.00
c = 45.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-04-23
  • Released Date: 2003-11-11
  • Deposition author(s): Luz, J.G., Rudolph, M.G., Wilson, I.A., Eisen, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update