[English] 日本語
![](img/lk-miru.gif)
- PDB-6t1l: Crystal structure of MLLT1 (ENL) YEATS domain in complexed with p... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6t1l | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MLLT1 (ENL) YEATS domain in complexed with piperazine-urea derivative 3 | ||||||
![]() | Protein ENL | ||||||
![]() | TRANSCRIPTION / YEATS domain / ENL / MLLT1 / chemical probe / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaikuad, A. / Heidenreich, D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fedorov, O. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural Insights into Interaction Mechanisms of Alternative Piperazine-urea YEATS Domain Binders in MLLT1. Authors: Ni, X. / Heidenreich, D. / Christott, T. / Bennett, J. / Moustakim, M. / Brennan, P.E. / Fedorov, O. / Knapp, S. / Chaikuad, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 642.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 644.4 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t1iC ![]() 6t1jC ![]() 6t1mC ![]() 6t1nC ![]() 6t1oC ![]() 6hq0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18225.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-M7N / ~{ | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG 3350, 0.2M sodium chloride, 0.1 M bis-tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2→49.08 Å / Num. obs: 11625 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 12.3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6hq0 Resolution: 2→46.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 17.074 / SU ML: 0.208 / SU R Cruickshank DPI: 0.2087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.185 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.24 Å2 / Biso mean: 55.775 Å2 / Biso min: 34.06 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→46.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -1.0761 Å / Origin y: -4.1452 Å / Origin z: 12.7038 Å
|