OCA Atlas for 2BDN

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

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 Diffraction

resolution

2.53 Å

Gene
Ontology

Chain	Function	Process	Component
A	G-protein coupled receptor b... protein kinase activity receptor binding cytokine activity chemokine activity heparin binding CCR2 chemokine receptor bind...	MAPK cascade angiogenesis response to hypoxia positive regulation of endot... monocyte chemotaxis protein phosphorylation cellular calcium ion homeost... chemotaxis inflammatory response humoral immune response activation of signaling prot... cytoskeleton organization cell adhesion signal transduction cell surface receptor signal... transforming growth factor b... G-protein coupled receptor s... G-protein coupled receptor s... JAK-STAT cascade aging regulation of cell shape response to heat response to wounding response to mechanical stimu... response to bacterium organ morphogenesis response to gamma radiation regulation of vascular endot... positive regulation of macro... response to activity negative regulation of angio... viral genome replication cytokine-mediated signaling ... cellular homeostasis neutrophil chemotaxis endoplasmic reticulum unfold... organ regeneration lipopolysaccharide-mediated ... response to lipopolysacchari... response to progesterone sti... response to vitamin B3 helper T cell extravasation response to drug negative regulation of apopt... response to amino acid stimu... protein kinase B signaling c... astrocyte cell migration cellular protein metabolic p... cellular response to fibrobl... response to ethanol response to antibiotic vascular endothelial growth ... macrophage chemotaxis lymphocyte chemotaxis positive regulation of synap... positive regulation of T cel... response to glucocorticoid s... positive regulation of nitri... maternal process involved in... chemokine-mediated signaling... cellular response to lipopol... cellular response to interfe... cellular response to interle... cellular response to tumor n... cellular response to organic... positive regulation of immun... positive regulation of apopt... negative regulation of natur...	extracellular region extracellular space cytoplasm neuronal cell body

Primary reference

Structure 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 (201 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.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [2bdn_H] [2bdn_L]

SWISS-PROT database: [P13500]

Domain organization of [CCL2_HUMAN] by SWISSPFAM

Domains found in 2BDN: [IG_like] [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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