2RAM	Transcription Dna	date	Nov 23, 1997
title	A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer
authors	Y.Q.Chen, S.Ghosh, G.Ghosh
compound		source
Molecule: Dna (5'-D(Cpgpgpcptpgpgpapapaptp(5iu) Pcpcpapgpcpcpg)-3'); Chain: C, D Engineered: Yes		Synthetic: Yes
Molecule: Protein (Transcription Factor Nf-Kb P65) Chain: A, B Fragment: P65 Residues 19 - 291 Synonym: Rela Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.213 R_Free 0.308
crystal cell	length a length b length c angle alpha angle beta angle gamma 65.810 80.620 167.800 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	5IU, DTV	enzyme
related structures	by homologous chain: 1IKN, 1K3Z
Gene Ontology	Chain Function Process Component A, B
Primary reference	A novel DNA recognition mode by the NF-kappa B p65 homodimer., Chen YQ, Ghosh S, Ghosh G, Nat Struct Biol 1998 Jan;5(1):67-73. PMID:9437432

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk] Biological Unit Coordinates (2ram.pdb1.gz) 106 Kb LPC: Ligand-Protein Contacts for 2RAM CSU: Contacts of Structural Units for 2RAM Likely Quarternary Molecular Structure file(s) for 2RAM Structure Factors (258 Kb) Retrieve 2RAM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2RAM from S2C, [Save to disk] Re-refined 2ram structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2RAM 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 2RAM

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 2RAM, from MSDmotif at EBI Genome occurence of 2RAM's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d2rama2, region A:19-191 [Jmol] [rasmolscript] [script source]     - Domain d2rama1, region A:192-291 [Jmol] [rasmolscript] [script source]     - Domain d2ramb2, region B:19-191 [Jmol] [rasmolscript] [script source]     - Domain d2ramb1, region B:192-291 [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: [2ram_C] [2ram] [2ram_B] [2ram_A] [2ram_D] SWISS-PROT database: [Q04207] Domain organization of [TF65_MOUSE] by SWISSPFAM Domain found in 2RAM: [IPT ] by SMART

Other resources with information on 2RAM

Community annotation for 2RAM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 2RAM from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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