3D1N	Transcription Regulator Dna	date	May 06, 2008
title	Structure Of Human Brn-5 Transcription Factor In Complex With Corticotrophin-Releasing Hormone Gene Promoter
authors	J.H.Pereira, S.C.Ha, S.H.Kim
compound		source
Molecule: 5'- D(Dapdgpdcpdapdtpdapdapdapdtpdapdapdtpdapda)- 3'; Chain: A, C, E, G Engineered: Yes		Synthetic: Yes
Molecule: 5'- D(Dtpdtpdapdtpdtpdapdtpdtpdtpdapdtpdgpdcpdt)- 3'; Chain: B, D, F, H Engineered: Yes		Synthetic: Yes
Molecule: Pou Domain, Class 6, Transcription Factor 1 Chain: I, J, K, L, M, N, O, P Fragment: Pou Domain (Unp Residues 142-292) Synonym: Mpou Homeobox Protein, Brain-Specific Homeoboxpou Domain Protein 5, Brain-5, Brn-5 Protein; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pou6f1, Brn5, Mpou, Tcfb1 Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3)Psjs1240 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pskb3
symmetry	Space Group: P 21 21 21	R_factor 0.212 R_Free 0.270
crystal cell	length a length b length c angle alpha angle beta angle gamma 100.298 112.060 181.504 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.51 Å
ligand	MSE	enzyme
Primary reference	Structure of human Brn-5 transcription factor in complex with CRH gene promoter., Pereira JH, Kim SH, J Struct Biol. 2009 May 15. PMID:19450691

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk] Biological Unit Coordinates (3d1n.pdb1.gz) 60 Kb Biological Unit Coordinates (3d1n.pdb2.gz) 51 Kb Biological Unit Coordinates (3d1n.pdb3.gz) 52 Kb Biological Unit Coordinates (3d1n.pdb4.gz) 52 Kb LPC: Ligand-Protein Contacts for 3D1N CSU: Contacts of Structural Units for 3D1N Likely Quarternary Molecular Structure file(s) for 3D1N Structure Factors (313 Kb) Retrieve 3D1N in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3D1N from S2C, [Save to disk] Re-refined 3d1n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3D1N 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 3D1N

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 3D1N, from MSDmotif at EBI Fold representative 3d1n from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3d1n_A] [3d1n_B] [3d1n_C] [3d1n_D] [3d1n_E] [3d1n_F] [3d1n_G] [3d1n_H] [3d1n_I] [3d1n_J] [3d1n_K] [3d1n_L] [3d1n_M] [3d1n_N] [3d1n_O] [3d1n_P] SWISS-PROT database: [Q14863] Domain organization of [PO6F1_HUMAN] by SWISSPFAM Domains found in 3D1N: [HOX] [POU ] by SMART Alignments of the sequence of 3D1N with the sequences similar proteins can be viewed for 3D1N's classification [PO6F1_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 [PO6F1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3D1N

Community annotation for 3D1N at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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