1KEG	Immune System Dna	date	Nov 15, 2001
title	Antibody 64m-2 Fab Complexed With Dtt(6-4)Tt
authors	H.Yokoyama, R.Mizutani, Y.Satow, K.Sato, Y.Komatsu, E.Ohtsuka, O.N
compound		source
Molecule: 5'-D(Tp(64t)Ptpt)-3' Chain: A Engineered: Yes		Synthetic: Yes Other_details: The Chain Was Synthesized By Coupling Thymid Both Sides Of Dt(6-4)T Which Was Purified From Ultraviolet- Dtpt.;
Molecule: Anti-(6-4) Photoproduct Antibody 64m-2 Fab (Light Chain: L		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Strain: Balbc Cell_line: Hybridoma
Molecule: Anti-(6-4) Photoproduct Antibody 64m-2 Fab (Heavy Chain: H		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Strain: Balbc Cell_line: Hybridoma
symmetry	Space Group: P 21 21 21	R_factor 0.201 R_Free 0.268
crystal cell	length a length b length c angle alpha angle beta angle gamma 73.567 137.274 49.615 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	64T, NI	enzyme
related structures	by homologous chain: 1AP2, 1C5D, 1NGP, 1R3I
Primary reference	Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides., Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y, Ohtsuka E, Nikaido O, Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):232-8. Epub 2012 Feb 7. PMID:22349224

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk] Biological Unit Coordinates (1keg.pdb1.gz) 70 Kb LPC: Ligand-Protein Contacts for 1KEG CSU: Contacts of Structural Units for 1KEG Likely Quarternary Molecular Structure file(s) for 1KEG Structure Factors (158 Kb) Retrieve 1KEG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1KEG from S2C, [Save to disk] Re-refined 1keg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1KEG 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 1KEG

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 1KEG, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1kegh1, region H:1-113 [Jmol] [rasmolscript] [script source]     - Domain d1kegh2, region H:114-228 [Jmol] [rasmolscript] [script source]     - Domain d1kegl1, region L:1-107 [Jmol] [rasmolscript] [script source]     - Domain d1kegl2, region L:108-212 [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: [1keg] [1keg_A] [1keg_L] [1keg_H] SWISS-PROT database: [P01863] Domain organization of [GCAA_MOUSE] by SWISSPFAM Domains found in 1KEG: [IG_like] [IGv ] by SMART

Other resources with information on 1KEG

Community annotation for 1KEG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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