8ZN7 | pdb_00008zn7

Crystal Structure of Designed Clock Protein KaiC

PDB DOI: https://doi.org/10.2210/pdb8ZN7/pdb

Classification: TRANSFERASE
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-26 Released: 2025-04-16
Deposition Author(s): Furuike, Y., Akiyama, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.272 (Depositor), 0.268 (DCC)
R-Value Work:
0.225 (Depositor), 0.223 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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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.

Macromolecule Content

Total Structure Weight: 348.93 kDa
Atom Count: 20,931
Modeled Residue Count: 2,791
Deposited Residue Count: 3,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KaiC	A [auth D] B [auth E] C [auth B] D [auth C] E [auth F] A [auth D], B [auth E], C [auth B], D [auth C], E [auth F], F [auth A]	512	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth E] SDF format, chain K [auth E] SDF format, chain H [auth D] SDF format, chain G [auth D] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth E] MOL2 format, chain K [auth E] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth E] mmCIF format, chain K [auth E] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] G [auth D] H [auth D] K [auth E] AA [auth A], BA [auth A], G [auth D], H [auth D], K [auth E], L [auth E], O [auth B], P [auth B], S [auth C], T [auth C], W [auth F], X [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain G [auth D] Focus chain H [auth D] Focus chain K [auth E] Focus chain L [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain G [auth D] Focus chain H [auth D] Focus chain K [auth E] Focus chain L [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth F] Focus chain X [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain DA [auth A] SDF format, chain CA [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A]	CA [auth A] DA [auth A] I [auth D] J [auth D] M [auth E] CA [auth A], DA [auth A], I [auth D], J [auth D], M [auth E], N [auth E], Q [auth B], R [auth B], U [auth C], V [auth C], Y [auth F], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain I [auth D] Focus chain J [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain I [auth D] Focus chain J [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth F] Focus chain Z [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A [auth D] B [auth E] C [auth B] D [auth C] E [auth F] A [auth D], B [auth E], C [auth B], D [auth C], E [auth F], F [auth A]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER