1NFD AN ALPHA-BETA T CELL RECEPTOR (TCR) HETERODIMER IN COMPLEX WITH AN ANTI-TCR FAB FRAGMENT DERIVED FROM A MITOGENIC ANTIBODY date
authors Wang, J.H., Lim, K., Smolyar, A., Teng, M.K., Sacchittini, J., Reinherz, E.L.
compound source
symmetry
R_factor
R_Free 0.309
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand NAG enzyme
related structures by homologous chain: 1G6R, 1KFA, 1L0X, 1OAY, 1TCR
Primary referenceAtomic structure of an alphabeta T cell receptor (TCR) heterodimer in complex with an anti-TCR fab fragment derived from a mitogenic antibody., Wang J, Lim K, Smolyar A, Teng M, Liu J, Tse AG, Liu J, Hussey RE, Chishti Y, Thomson CT, Sweet RM, Nathenson SG, Chang HC, Sacchettini JC, Reinherz EL, EMBO J 1998 Jan 2;17(1):10-26. PMID:9427737
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (1nfd.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (1nfd.pdb2.gz) 141 Kb
  • Biological Unit Coordinates (1nfd.pdb3.gz) 211 Kb
  • LPC: Ligand-Protein Contacts for 1NFD
  • CSU: Contacts of Structural Units for 1NFD
  • Likely Quarternary Molecular Structure file(s) for 1NFD
  • Retrieve 1NFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NFD from S2C, [Save to disk]
  • View 1NFD 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 1NFD
  • 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 1NFD, from MSDmotif at EBI
  • Genome occurence of 1NFD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nfda1, region A:1-117 [Jmol] [rasmolscript] [script source]
        - Domain d1nfda2, region A:118-213 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdb1, region B:1-117 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdb2, region B:118-247 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdc1, region C:1-117 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdc2, region C:118-213 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdd1, region D:1-117 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdd2, region D:118-247 [Jmol] [rasmolscript] [script source]
        - Domain d1nfde2, region E:108-215 [Jmol] [rasmolscript] [script source]
        - Domain d1nfde1, region E:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdf1, region F:1-114 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdf2, region F:115-228 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdg2, region G:108-215 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdg1, region G:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdh1, region H:1-114 [Jmol] [rasmolscript] [script source]
        - Domain d1nfdh2, region H:115-228 [Jmol] [rasmolscript] [script source]
  • Fold representative 1nfd 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: [1nfd_E] [1nfd_H] [1nfd_G] [1nfd_D] [1nfd_B] [1nfd] [1nfd_C] [1nfd_F] [1nfd_A]
  • SWISS-PROT database: [P01852]
  • Domain organization of [TCB1_MOUSE] by SWISSPFAM
  • Domains found in 1NFD: [IG] [IG_like] [IGc1] [IGv ] by SMART
  • Other resources with information on 1NFD
  • Community annotation for 1NFD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1NFD from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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