8ZN5 | pdb_00008zn5

Crystal Structure of Designed Clock Protein KaiC

PDB DOI: https://doi.org/10.2210/pdb8ZN5/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: 3.10 Å
R-Value Free:
0.329 (Depositor), 0.322 (DCC)
R-Value Work:
0.280 (Depositor), 0.278 (DCC)
R-Value Observed:
0.283 (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: 709.71 kDa
Atom Count: 36,725
Modeled Residue Count: 5,370
Deposited Residue Count: 6,216
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KaiC	A [auth B] B [auth C] C [auth F] D [auth A] E [auth D] A [auth B], B [auth C], C [auth F], D [auth A], E [auth D], F [auth E], G, H, I [auth K], J [auth L], K [auth I], L [auth J]	518	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
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain EB [auth J] SDF format, chain KA [auth G] SDF format, chain Q [auth C] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain XA [auth L] SDF format, chain WA [auth L] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain TA [auth K] SDF format, chain SA [auth K] SDF format, chain R [auth C] SDF format, chain PA [auth H] SDF format, chain OA [auth H] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain LA [auth G] SDF format, chain HA [auth E] SDF format, chain GA [auth E] SDF format, chain FB [auth J] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain BB [auth I] SDF format, chain AB [auth I] MOL2 format, chain EB [auth J] MOL2 format, chain KA [auth G] MOL2 format, chain Q [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth L] MOL2 format, chain WA [auth L] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain TA [auth K] MOL2 format, chain SA [auth K] MOL2 format, chain R [auth C] MOL2 format, chain PA [auth H] MOL2 format, chain OA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain FB [auth J] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain AB [auth I] mmCIF format, chain EB [auth J] mmCIF format, chain KA [auth G] mmCIF format, chain Q [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth L] mmCIF format, chain WA [auth L] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain TA [auth K] mmCIF format, chain SA [auth K] mmCIF format, chain R [auth C] mmCIF format, chain PA [auth H] mmCIF format, chain OA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain FB [auth J] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain AB [auth I]	AB [auth I] BB [auth I] CA [auth D] DA [auth D] EB [auth J] AB [auth I], BB [auth I], CA [auth D], DA [auth D], EB [auth J], FB [auth J], GA [auth E], HA [auth E], KA [auth G], LA [auth G], M [auth B], N [auth B], OA [auth H], PA [auth H], Q [auth C], R [auth C], SA [auth K], TA [auth K], U [auth F], V [auth F], WA [auth L], XA [auth L], Y [auth A], Z [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain U [auth F] Focus chain V [auth F] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain U [auth F] Focus chain V [auth F] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain Y [auth A] Focus chain Z [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain ZA [auth L] SDF format, chain YA [auth L] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain VA [auth K] SDF format, chain UA [auth K] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain RA [auth H] SDF format, chain QA [auth H] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain NA [auth G] SDF format, chain MA [auth G] SDF format, chain JA [auth E] SDF format, chain IA [auth E] SDF format, chain HB [auth J] SDF format, chain GB [auth J] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DB [auth I] SDF format, chain CB [auth I] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain ZA [auth L] MOL2 format, chain YA [auth L] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain VA [auth K] MOL2 format, chain UA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth H] MOL2 format, chain QA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain JA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain HB [auth J] MOL2 format, chain GB [auth J] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth I] MOL2 format, chain CB [auth I] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain ZA [auth L] mmCIF format, chain YA [auth L] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain VA [auth K] mmCIF format, chain UA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth H] mmCIF format, chain QA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain JA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain HB [auth J] mmCIF format, chain GB [auth J] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth I] mmCIF format, chain CB [auth I] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CB [auth I] DB [auth I] EA [auth D] AA [auth A], BA [auth A], CB [auth I], DB [auth I], EA [auth D], FA [auth D], GB [auth J], HB [auth J], IA [auth E], JA [auth E], MA [auth G], NA [auth G], O [auth B], P [auth B], QA [auth H], RA [auth H], S [auth C], T [auth C], UA [auth K], VA [auth K], W [auth F], X [auth F], YA [auth L], ZA [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain UA [auth K] Focus chain VA [auth K] Focus chain W [auth F] Focus chain X [auth F] Focus chain YA [auth L] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain UA [auth K] Focus chain VA [auth K] Focus chain W [auth F] Focus chain X [auth F] Focus chain YA [auth L] Focus chain ZA [auth L]