5YTT

Crystal structure of YB1 cold-shock domain in complex with UCAUGU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of YB1 cold-shock domain in complex with

Yang, X.Huang, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclease-sensitive element-binding protein 1
A
83Homo sapiensMutation(s): 0 
Gene Names: YBX1 (NSEP1, YB1)
Find proteins for P67809 (Homo sapiens)
Go to Gene View: YBX1
Go to UniProtKB:  P67809
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*CP*AP*UP*GP*U)-3')B7synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 66.218α = 90.00
b = 66.218β = 90.00
c = 36.080γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-20 
  • Released Date: 2018-12-05 
  • Deposition Author(s): Yang, X., Huang, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91640102
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08010202

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release