1YB5

Crystal structure of human Zeta-Crystallin with bound NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.207 (Depositor) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of human Zeta-Crystallin at 1.85A

Debreczeni, J.Berridge, G.Kavanagh, K.Colbrook, S.Bray, J.Williams, L.Oppermann, U.Sundstrom, M.Arrowsmith, C.Edwards, A.Gileadi, O.von Delft, F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Quinone oxidoreductase
A, B
351Homo sapiensMutation(s): 0 
Gene Names: CRYZ
EC: 1.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q08257 (Homo sapiens)
Explore Q08257 
Go to UniProtKB:  Q08257
PHAROS:  Q08257
GTEx:  ENSG00000116791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08257
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
L [auth B],
M [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.207 (Depositor) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.484α = 90
b = 110.239β = 90
c = 77.253γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations