+Open data
-Basic information
Entry | Database: PDB / ID: 1qry | ||||||
---|---|---|---|---|---|---|---|
Title | Homeobox protein VND (ventral nervous system defective protein) | ||||||
Components | PROTEIN (HOMEOBOX VENTRAL NERVOUS SYSTEM DEFECTIVE PROTEIN) | ||||||
Keywords | DNA BINDING PROTEIN / HELIX-TURN-HELIX / DNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information neuroblast development / neuroblast fate determination / glial cell development / brain development / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II ...neuroblast development / neuroblast fate determination / glial cell development / brain development / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Xiang, B. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation. Authors: Hwang, K.J. / Xiang, B. / Gruschus, J.M. / Nam, K.Y. / No, K.T. / Nirenberg, M. / Ferretti, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qry.cif.gz | 539.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qry.ent.gz | 467.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/1qry ftp://data.pdbj.org/pub/pdb/validation_reports/qr/1qry | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9747.162 Da / Num. of mol.: 1 / Fragment: vnd/NK2 homeodomain / Mutation: A35T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)PLYSS / References: UniProt: P22808 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||
NMR details | Text: 3D 15N EDITED NOESY-HSQC, 4D 15N/13C EDITED HMQC-NOESY-HSQC, AND 4D 13C/13C EDITED HMQC-NOESY-HSQC WERE USED FOR OBTAINING NOE RESTRAINTS. |
-Sample preparation
Details |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
Sample conditions | pH: 6.8 / Pressure: AMBIENT / Temperature: 308 K | ||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz |
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON 1146 NOE-DERIVED DISTANCE RESTRAINTS AND 43 DIHEDRAL ANGLE RESTRAINTS. | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 100 / Conformers submitted total number: 20 |