1C3D Complement date May 19, 1998
title X-Ray Crystal Structure Of C3d: A C3 Fragment And Ligand For Complement Receptor 2
authors B.Nagar, R.G.Jones, R.J.Diefenbach, D.E.Isenman, J.M.Rini
compound source
Molecule: C3d
Chain: A
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Bl21
Cellular_location: Serum
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Pet
Expression_system_vector: Pet 15b
Expression_system_plasmid: Bl21
symmetry Space Group: P 21 21 21
R_factor 0.188 R_Free 0.230
length a length b length c angle alpha angle beta angle gamma
60.820 64.378 87.160 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand GOL enzyme
related structures by homologous chain: 1QQF, 1QSJ

Primary referenceX-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2., Nagar B, Jones RG, Diefenbach RJ, Isenman DE, Rini JM, Science 1998 May 22;280(5367):1277-81. PMID:9596584
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (1c3d.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 1C3D
  • CSU: Contacts of Structural Units for 1C3D
  • Likely Quarternary Molecular Structure file(s) for 1C3D
  • Retrieve 1C3D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1C3D from S2C, [Save to disk]
  • View 1C3D 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 1C3D
  • 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 1C3D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1c3d__, region [Jmol] [rasmolscript] [script source]
  • Fold representative 1c3d 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: [1c3d_A] [1c3d]
  • SWISS-PROT database: [P01024]
  • Domain organization of [CO3_HUMAN] by SWISSPFAM
  • Domain found in 1C3D: [Thiol-ester_cl ] by SMART
  • Other resources with information on 1C3D
  • Community annotation for 1C3D 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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