1RD4 Immune System date Nov 05, 2003
title An Allosteric Inhibitor Of Lfa-1 Bound To Its I-Domain
authors M.P.Crump, T.A.Ceska, L.Spyracopoulos, A.Henry, S.C.Archibald, R.Alexander, R.J.Taylor, S.C.Findlow, J.O'Connell, M.K.Robinson
compound source
Molecule: Integrin Alpha-L
Chain: A, B, C, D
Fragment: I Domain, Residues 125-311
Synonym: Leukocyte Adhesion Glycoprotein Lfa-1 Alpha Chain, Function Associated Molecule 1 Alpha Chain, Cd11a;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Itgal, Cd11a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.236 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.960 64.410 66.210 74.21 90.00 87.26
method X-Ray Diffractionresolution 2.40 Å
ligand L08 enzyme
related structures by homologous chain: 1MQA, 1XDD
Primary referenceStructure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry., Crump MP, Ceska TA, Spyracopoulos L, Henry A, Archibald SC, Alexander R, Taylor RJ, Findlow SC, O'Connell J, Robinson MK, Shock A, Biochemistry 2004 Mar 9;43(9):2394-404. PMID:14992576
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk]
  • Biological Unit Coordinates (1rd4.pdb1.gz) 31 Kb
  • Biological Unit Coordinates (1rd4.pdb2.gz) 32 Kb
  • Biological Unit Coordinates (1rd4.pdb3.gz) 32 Kb
  • Biological Unit Coordinates (1rd4.pdb4.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 1RD4
  • CSU: Contacts of Structural Units for 1RD4
  • Likely Quarternary Molecular Structure file(s) for 1RD4
  • Retrieve 1RD4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RD4 from S2C, [Save to disk]
    • View 1RD4 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 1RD4
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RD4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rd4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rd4b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1rd4c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1rd4d_, region D [Jmol] [rasmolscript] [script source]
  • 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: [1rd4_A] [1rd4_C] [1rd4_B] [1rd4_D] [1rd4]
  • SWISS-PROT database: [P20701]
  • Domain organization of [ITAL_HUMAN] by SWISSPFAM
  • Domain found in 1RD4: [VWA ] by SMART
    • Other resources with information on 1RD4
  • Community annotation for 1RD4 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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