1HYR Immune System date Jan 21, 2001
title Crystal Structure Of Human Mica In Complex With Natural Killer Cell Receptor Nkg2d
authors P.Li, R.K.Strong
compound source
Molecule: Nkg2-D Type II Integral Membrane Protein
Chain: B, A
Fragment: Extracellular Domain (Residues 80 To 216)
Synonym: Nkg2d
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cellular_location: Cell Surface
Gene: Nkg2d
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Mhc Class I Chain-Related Protein A
Chain: C
Fragment: Extracellular Domain (Residues 1 To 274)
Synonym: Mic-A, Mic, Perb11
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mica-001
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11
symmetry Space Group: P 4 21 2
R_factor 0.227 R_Free 0.282
length a length b length c angle alpha angle beta angle gamma
122.780 122.780 101.820 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
related structures by homologous chain: 1B3J, 1JE6, 1KCG
A, B

Primary referenceComplex structure of the activating immunoreceptor NKG2D and its MHC class I-like ligand MICA., Li P, Morris DL, Willcox BE, Steinle A, Spies T, Strong RK, Nat Immunol 2001 May;2(5):443-51. PMID:11323699
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (1hyr.pdb1.gz) 82 Kb
  • CSU: Contacts of Structural Units for 1HYR
  • Likely Quarternary Molecular Structure file(s) for 1HYR
  • Retrieve 1HYR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1HYR from S2C, [Save to disk]
  • View 1HYR in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1HYR
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1HYR, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1hyra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1hyrb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1hyrc2, region C:0-180 [Jmol] [rasmolscript] [script source]
        - Domain d1hyrc1, region C:181-274 [Jmol] [rasmolscript] [script source]
  • Fold representative 1hyr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1hyr_B] [1hyr_A] [1hyr] [1hyr_C]
  • SWISS-PROT database: [Q29983] [P26718]
  • Domain organization of [MICA_HUMAN] [NKG2D_HUMAN] by SWISSPFAM
  • Domains found in 1HYR: [CLECT] [IGc1 ] by SMART
  • Other resources with information on 1HYR
  • Community annotation for 1HYR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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