2DQU	Immune System	date	May 30, 2006
title	Crystal Form II: High Resolution Crystal Structure Of The Co The Hydrolytic Antibody Fab 6d9 And A Transition-State Anal
authors	O.Kristensen, D.G.Vassylyev, F.Tanaka, N.Ito, K.Morikawa, I.Fujii
compound		source
Molecule: Immunoglobulin 6d9 Chain: L Fragment: Fab Fragment Synonym: Catalytic Antibody 6d9		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Cell_line: 6d9 Murine-Murine Hybridoma Secretion: Ascites Fluid
Molecule: Immunoglobulin 6d9 Chain: H Fragment: Fab Fragment Synonym: Catalytic Antibody 6d9		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Cell_line: 6d9 Murine-Murine Hybridoma Secretion: Ascites Fluid
symmetry	Space Group: P 1 21 1	R_factor 0.207 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 58.700 63.040 56.560 90.00 98.75 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	CPD	enzyme
note	2DQU supersedes 1HYY
Gene Ontology	Chain Function Process Component H L
Primary reference	Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis., Oda M, Ito N, Tsumuraya T, Suzuki K, Sakakura M, Fujii I, J Mol Biol. 2007 May 25;369(1):198-209. Epub 2007 Mar 15. PMID:17428500

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk] Biological Unit Coordinates (2dqu.pdb1.gz) 74 Kb LPC: Ligand-Protein Contacts for 2DQU CSU: Contacts of Structural Units for 2DQU Likely Quarternary Molecular Structure file(s) for 2DQU Structure Factors (237 Kb) Retrieve 2DQU in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DQU from S2C, [Save to disk] Re-refined 2dqu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DQU 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 2DQU

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 2DQU, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2dqu] [2dqu_H] [2dqu_L] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 2DQU: [IG_like] [IGv ] by SMART

Other resources with information on 2DQU

Community annotation for 2DQU 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

---