6VGD	Transcription	date	Jan 07, 2020
title	Crystal Structure Of The Dna Binding Domain (Dbd) Of Human F The Complex Of The Dbd Of Human Runx2 With Core Binding Fac (Cbfb), In Complex With 16mer Dna Cagaggatgtggcttc
authors	C.Hou, O.V.Tsodikov
compound		source
Molecule: Friend Leukemia Integration 1 Transcription Facto Chain: A Fragment: Dna Binding Domain Synonym: Proto-Oncogene Fli-1,Transcription Factor Ergb Engineered: Yes Other_details: The N-Terminal Gphm Is Left From The Affinit After Its Cleavage.;		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Fli1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008
Molecule: Dna (5'- D(Pcpapgpapgpgpaptpgptpgpgpcptptpc)-3'); Chain: B Engineered: Yes Other_details: Synthetic Dna		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Dna (5'- D(Pgpapapgpcpcpapcpaptpcpcptpcptpg)-3'); Chain: C Engineered: Yes Other_details: Synthetic Dna		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Runt-Related Transcription Factor 2 Chain: D Fragment: Dna Binding Domain Synonym: Acute Myeloid Leukemia 3 Protein,Core-Binding Fact Alpha-1,Cbf-Alpha-1,Oncogene Aml-3,Osteoblast-Specific Tran Factor 2,Osf-2,Polyomavirus Enhancer-Binding Protein 2 Alph Subunit,Pebp2-Alpha A,Sl3-3 Enhancer Factor 1 Alpha A Subun Core-Binding Factor Alpha A Subunit; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Runx2, Aml3, Cbfa1, Osf2, Pebp2a Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008
Molecule: Core-Binding Factor Subunit Beta Chain: G Synonym: Cbf-Beta,Polyomavirus Enhancer-Binding Protein 2 B Subunit,Pebp2-Beta,Sl3-3 Enhancer Factor 1 Subunit Beta,Sl3 Binding Factor Beta Subunit; Engineered: Yes Other_details: The N-Terminal Region Agsshhhhhhsqdp Is A Cl Affinity Tag.		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cbfb Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008
symmetry	Space Group: P 62 2 2	R_factor 0.295 R_Free 0.293
crystal cell	length a length b length c angle alpha angle beta angle gamma 104.513 104.513 322.040 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	4.20 Å

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk] Biological Unit Coordinates (6vgd.pdb1.gz) 146 Kb CSU: Contacts of Structural Units for 6VGD Structure Factors (232 Kb) Retrieve 6VGD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 6VGD from S2C, [Save to disk]

View 6VGD 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 6VGD

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [6vgd_A] [6vgd_G] [6vgd_D] [6vgd_B] [6vgd_C] SWISS-PROT database: Domain organization of by SWISSPFAM

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