8ZN6 | pdb_00008zn6

Crystal Structure of Designed Clock Protein KaiC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.292 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal Structure of Designed Clock Protein KaiC

Furuike, Y.Akiyama, S.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KaiCA [auth F],
B [auth A],
I [auth K],
L [auth J]
515synthetic constructMutation(s): 0 
EC: 2.7.11.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KaiC515synthetic constructMutation(s): 0 
EC: 2.7.11.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
BA [auth B]
BB [auth J]
CA [auth B]
CB [auth J]
EA [auth C]
BA [auth B],
BB [auth J],
CA [auth B],
CB [auth J],
EA [auth C],
FA [auth C],
HA [auth G],
IA [auth G],
LA [auth H],
M [auth F],
MA [auth H],
N [auth F],
PA [auth K],
Q [auth A],
QA [auth K],
R [auth A],
TA [auth L],
U [auth D],
UA [auth L],
V [auth D],
X [auth E],
XA [auth I],
Y [auth E],
YA [auth I]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth E]
AB [auth I]
DA [auth B]
DB [auth J]
GA [auth C]
AA [auth E],
AB [auth I],
DA [auth B],
DB [auth J],
GA [auth C],
JA [auth G],
KA [auth G],
NA [auth H],
O [auth F],
OA [auth H],
P [auth F],
RA [auth K],
S [auth A],
SA [auth K],
T [auth A],
VA [auth L],
W [auth D],
WA [auth L],
Z [auth E],
ZA [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth F],
B [auth A],
I [auth K],
L [auth J]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.292 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.76α = 77.97
b = 110.27β = 87.25
c = 166.89γ = 82.41
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release