8ZN6 | pdb_00008zn6

Crystal Structure of Designed Clock Protein KaiC

PDB DOI: https://doi.org/10.2210/pdb8ZN6/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: 2.94 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.

Macromolecule Content

Total Structure Weight: 703.59 kDa
Atom Count: 41,205
Modeled Residue Count: 5,629
Deposited Residue Count: 6,180
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KaiC	A [auth F], B [auth A], I [auth K], L [auth J]	515	synthetic construct	Mutation(s): 0 EC: 2.7.11.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KaiC	C [auth D] D [auth E] E [auth B] F [auth C] G C [auth D], D [auth E], E [auth B], F [auth C], G, H, J [auth L], K [auth I]	515	synthetic construct	Mutation(s): 0 EC: 2.7.11.1
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 BA [auth B] SDF format, chain CA [auth B] SDF format, chain CB [auth J] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain HA [auth G] SDF format, chain LA [auth H] SDF format, chain M [auth F] SDF format, chain MA [auth H] SDF format, chain PA [auth K] SDF format, chain Q [auth A] SDF format, chain QA [auth K] SDF format, chain R [auth A] SDF format, chain TA [auth L] SDF format, chain U [auth D] SDF format, chain UA [auth L] SDF format, chain V [auth D] SDF format, chain XA [auth I] SDF format, chain Y [auth E] SDF format, chain YA [auth I] SDF format, chain X [auth E] SDF format, chain N [auth F] SDF format, chain IA [auth G] SDF format, chain BB [auth J] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth J] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain HA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth F] MOL2 format, chain MA [auth H] MOL2 format, chain PA [auth K] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth K] MOL2 format, chain R [auth A] MOL2 format, chain TA [auth L] MOL2 format, chain U [auth D] MOL2 format, chain UA [auth L] MOL2 format, chain V [auth D] MOL2 format, chain XA [auth I] MOL2 format, chain Y [auth E] MOL2 format, chain YA [auth I] MOL2 format, chain X [auth E] MOL2 format, chain N [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain BB [auth J] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth J] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain HA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain M [auth F] mmCIF format, chain MA [auth H] mmCIF format, chain PA [auth K] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth K] mmCIF format, chain R [auth A] mmCIF format, chain TA [auth L] mmCIF format, chain U [auth D] mmCIF format, chain UA [auth L] mmCIF format, chain V [auth D] mmCIF format, chain XA [auth I] mmCIF format, chain Y [auth E] mmCIF format, chain YA [auth I] mmCIF format, chain X [auth E] mmCIF format, chain N [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain BB [auth J]	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		Interactions Focus chain BA [auth B] Focus chain BB [auth J] Focus chain CA [auth B] Focus chain CB [auth J] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain M [auth F] Focus chain MA [auth H] Focus chain N [auth F] Focus chain PA [auth K] Focus chain Q [auth A] Focus chain QA [auth K] Focus chain R [auth A] Focus chain TA [auth L] Focus chain U [auth D] Focus chain UA [auth L] Focus chain V [auth D] Focus chain X [auth E] Focus chain XA [auth I] Focus chain Y [auth E] Focus chain YA [auth I] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth J] Focus chain CA [auth B] Focus chain CB [auth J] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain M [auth F] Focus chain MA [auth H] Focus chain N [auth F] Focus chain PA [auth K] Focus chain Q [auth A] Focus chain QA [auth K] Focus chain R [auth A] Focus chain TA [auth L] Focus chain U [auth D] Focus chain UA [auth L] Focus chain V [auth D] Focus chain X [auth E] Focus chain XA [auth I] Focus chain Y [auth E] Focus chain YA [auth I]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain AB [auth I] SDF format, chain DA [auth B] SDF format, chain DB [auth J] SDF format, chain GA [auth C] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain OA [auth H] SDF format, chain RA [auth K] SDF format, chain S [auth A] SDF format, chain SA [auth K] SDF format, chain T [auth A] SDF format, chain VA [auth L] SDF format, chain Z [auth E] SDF format, chain ZA [auth I] SDF format, chain WA [auth L] SDF format, chain W [auth D] SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain NA [auth H] MOL2 format, chain AA [auth E] MOL2 format, chain AB [auth I] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain RA [auth K] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth L] MOL2 format, chain Z [auth E] MOL2 format, chain ZA [auth I] MOL2 format, chain WA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain NA [auth H] mmCIF format, chain AA [auth E] mmCIF format, chain AB [auth I] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain OA [auth H] mmCIF format, chain RA [auth K] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth K] mmCIF format, chain T [auth A] mmCIF format, chain VA [auth L] mmCIF format, chain Z [auth E] mmCIF format, chain ZA [auth I] mmCIF format, chain WA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain NA [auth H]	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		Interactions Focus chain AA [auth E] Focus chain AB [auth I] Focus chain DA [auth B] Focus chain DB [auth J] Focus chain GA [auth C] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain O [auth F] Focus chain OA [auth H] Focus chain P [auth F] Focus chain RA [auth K] Focus chain S [auth A] Focus chain SA [auth K] Focus chain T [auth A] Focus chain VA [auth L] Focus chain W [auth D] Focus chain WA [auth L] Focus chain Z [auth E] Focus chain ZA [auth I] Interactions & Density Focus chain AA [auth E] Focus chain AB [auth I] Focus chain DA [auth B] Focus chain DB [auth J] Focus chain GA [auth C] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain O [auth F] Focus chain OA [auth H] Focus chain P [auth F] Focus chain RA [auth K] Focus chain S [auth A] Focus chain SA [auth K] Focus chain T [auth A] Focus chain VA [auth L] Focus chain W [auth D] Focus chain WA [auth L] Focus chain Z [auth E] Focus chain ZA [auth I]