1RAM	Transcription Dna	date	Nov 22, 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(Cpgpgpcptpgpgpapapaptptptpcpcpapgpcpcp Chain: C, D Engineered: Yes		Synthetic: Yes
Molecule: Protein (Transcription Factor Nf-Kb P65) Chain: A, B Fragment: P65 Subunit, Residues 19 - 291 Synonym: Rela, Nuclear Factor Kappa-B Chain P65, Avian Reticuloendotheliosis Viral (V-Rel) Oncogene Homolog A; 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 0.222 R_Free 0.324
crystal cell	length a length b length c angle alpha angle beta angle gamma 65.690 81.080 167.560 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	DTT	enzyme
related structures	by homologous chain: 1K3Z, 1NFI
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] (109 Kb) [Save to disk] Biological Unit Coordinates (1ram.pdb1.gz) 104 Kb LPC: Ligand-Protein Contacts for 1RAM CSU: Contacts of Structural Units for 1RAM Likely Quarternary Molecular Structure file(s) for 1RAM Structure Factors (239 Kb) Retrieve 1RAM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RAM from S2C, [Save to disk] Re-refined 1ram structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RAM 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 1RAM

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 1RAM, from MSDmotif at EBI Genome occurence of 1RAM's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rama2, region A:19-191 [Jmol] [rasmolscript] [script source]     - Domain d1rama1, region A:192-291 [Jmol] [rasmolscript] [script source]     - Domain d1ramb2, region B:19-191 [Jmol] [rasmolscript] [script source]     - Domain d1ramb1, 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: [1ram] [1ram_C] [1ram_B] [1ram_D] [1ram_A] SWISS-PROT database: [Q04207] Domain organization of [TF65_MOUSE] by SWISSPFAM Domain found in 1RAM: [IPT ] by SMART

Other resources with information on 1RAM

Community annotation for 1RAM 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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