1AFD Lectin date Nov 03, 1995
title Structural Basis Of Galactose Recognition In C-Type Animal L
authors A.R.Kolatkar, W.I.Weis
compound source
Molecule: Mannose-Binding Protein-A
Chain: 1, 2, 3
Fragment: Clostripain Fragment (Residues 73 - 226)
Synonym: Cl-Qpdwg
Engineered: Yes
Mutation: Yes
Other_details: Ph 8.0, Data Collected At 100k, 20% 2-Methyl Pentanediol (Cryoprotectant)
Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Piniiiompa2
Other_details: The Bacterially Expressed Material Is Digest Clostripain To Produce The Protein Used In The Crystal Stru Analysis
symmetry Space Group: C 1 2 1
R_factor 0.234 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.400 84.700 98.000 90.00 105.40 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CA, CL enzyme
related structures by homologous chain: 1AFA, 1KMB
Gene
Ontology
ChainFunctionProcessComponent
1, 3, 2


Primary referenceStructural basis of galactose recognition by C-type animal lectins., Kolatkar AR, Weis WI, J Biol Chem 1996 Mar 22;271(12):6679-85. PMID:8636086
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (1afd.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 1AFD
  • CSU: Contacts of Structural Units for 1AFD
  • Likely Quarternary Molecular Structure file(s) for 1AFD
  • Structure Factors (463 Kb)
  • Retrieve 1AFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1AFD from S2C, [Save to disk]
  • Re-refined 1afd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1AFD 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 1AFD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1AFD, from MSDmotif at EBI
  • Genome occurence of 1AFD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1afd11, region 1:105-226 [Jmol] [rasmolscript] [script source]
        - Domain d1afd12, region 1:73-104 [Jmol] [rasmolscript] [script source]
        - Domain d1afd21, region 2:105-226 [Jmol] [rasmolscript] [script source]
        - Domain d1afd22, region 2:73-104 [Jmol] [rasmolscript] [script source]
        - Domain d1afd31, region 3:105-226 [Jmol] [rasmolscript] [script source]
        - Domain d1afd32, region 3:73-104 [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: [1afd] [1afd_2] [1afd_3] [1afd_1]
  • SWISS-PROT database: [P19999]
  • Domain organization of [MBL1_RAT] by SWISSPFAM
  • Domain found in 1AFD: [CLECT ] by SMART
  • Other resources with information on 1AFD
  • Community annotation for 1AFD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science