1NKQ

Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crtystal Structure of Yeast Hypothetical Protein YNQ8_YEAST

Eswaramoorthy, S.Kumaran, D.Daniels, B.Studier, F.W.Swaminathan, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
A, B, C, D, E, F
A, B, C, D, E, F
259Saccharomyces cerevisiaeMutation(s): 6 
Gene Names: YNL168C or N1696
EC: 3
UniProt
Find proteins for P53889 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53889 
Go to UniProtKB:  P53889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53889
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
L [auth B],
N [auth B],
O [auth B],
H [auth A],
I [auth A],
L [auth B],
N [auth B],
O [auth B],
S [auth C],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
J [auth A],
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
W [auth D],
X [auth D]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth F],
G [auth A],
M [auth B],
R [auth C],
V [auth D],
CA [auth F],
G [auth A],
M [auth B],
R [auth C],
V [auth D],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.705α = 90
b = 85.99β = 90
c = 316.704γ = 90
Software Package:
Software NamePurpose
MARMADdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SHARPphasing
CNSrefinement
MARMADdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary