+
Open data
-
Basic information
Entry | Database: PDB / ID: 5x3p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the UBX domain of human UBXD7 | ||||||
![]() | UBX domain-containing protein 7 | ||||||
![]() | PROTEIN BINDING / UBXD7 / p97 | ||||||
Function / homology | ![]() VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin binding / KEAP1-NFE2L2 pathway / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, T. / Li, Z. / Wang, Y. / Xu, M. | ||||||
![]() | ![]() Title: Crystal structures of the UBX domain of human UBXD7 and its complex with p97 ATPase Authors: Li, Z.H. / Wang, Y. / Xu, M. / Jiang, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 88.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.1 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 9633.721 Da / Num. of mol.: 3 / Fragment: UNP residues 410-489 / Mutation: L472M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.22 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion Details: 0.1M Tris pH 8.8, 35% v/v Polyethylene glycol 400, 0.1M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→38.24 Å / Num. obs: 14643 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.048 / Net I/σ(I): 16.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.999→38.24 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 16.5605 Å / Origin y: 75.6638 Å / Origin z: 7.0928 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |