2BDN Immune System date Oct 20, 2005
title Crystal Structure Of Human Mcp-1 Bound To A Blocking Antibody, 11k2
authors P.A.Boriack-Sjodin, M.Rushe, C.Reid, M Jarpe, H Van Vlijmen, V.Bailly
compound source
Molecule: Small Inducible Cytokine A2
Chain: A
Fragment: Monocyte Chemotactic Protein -1
Synonym: Ccl2, Monocyte Chemotactic Protein 1, Mcp-1, Monocyte Chemoattractant Protein 1, Monocyte Chemotactic And Activating Factor, Mcaf, Monocyte Secretory Protein Je, Hc11;
Engineered: Yes
Synthetic: Yes
Other_details: Chemically Synthesized. This Sequence Occurs Naturally In Humans;

Molecule: Antibody Light Chain 11k2
Chain: L
Fragment: Fab Fragment
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell: Murine Hybridoma Cells

Molecule: Antibody Heavy Chain 11k2
Chain: H
Fragment: Fab Fragment
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell: Murine Hybridoma Cells
symmetry Space Group: C 2 2 21
R_factor 0.219 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.360 89.100 176.240 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.53 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure activity relationships of monocyte chemoattractant proteins in complex with a blocking antibody., Reid C, Rushe M, Jarpe M, van Vlijmen H, Dolinski B, Qian F, Cachero TG, Cuervo H, Yanachkova M, Nwankwo C, Wang X, Etienne N, Garber E, Bailly V, de Fougerolles A, Boriack-Sjodin PA, Protein Eng Des Sel. 2006 May 8;. PMID:16682434
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (2bdn.pdb1.gz) 157 Kb
  • CSU: Contacts of Structural Units for 2BDN
  • Likely Quarternary Molecular Structure file(s) for 2BDN
  • Structure Factors (191 Kb)
  • Retrieve 2BDN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BDN from S2C, [Save to disk]
  • Re-refined 2bdn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BDN 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 2BDN
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2BDN, from MSDmotif at EBI
  • Fold representative 2bdn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bdn] [2bdn_H] [2bdn_L] [2bdn_A]
  • SWISS-PROT database: [P13500]
  • Domain organization of [CCL2_HUMAN] by SWISSPFAM
  • Domains found in 2BDN: [IGc1] [IGv] [SCY ] by SMART
  • Alignments of the sequence of 2BDN with the sequences similar proteins can be viewed for 2BDN's classification [CCL2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CCL2_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2BDN
  • Community annotation for 2BDN 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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