9S6L | pdb_00009s6l

Structure of C. tepidum Rel in an open state in complex with APCPP and GDP

PDB DOI: https://doi.org/10.2210/pdb9S6L/pdb

Classification: TRANSFERASE
Organism(s): Chlorobaculum tepidum
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-08-01 Released: 2026-10-28
Deposition Author(s): Garcia-Pino, A., Talavera, A.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.214 (Depositor), 0.215 (DCC)
R-Value Observed:
0.215 (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

Structure of C. tepidum Rel in an open state in complex with APCPP and GDP

Garcia-Pino, A., Talavera Perez, A.

To be published.

Macromolecule Content

Total Structure Weight: 165.57 kDa
Atom Count: 10,967
Modeled Residue Count: 1,343
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP pyrophosphokinase	A, B, C, D	347	Chlorobaculum tepidum	Mutation(s): 0 Gene Names: relA, CT1545 EC: 2.7.6.5
UniProt
Find proteins for Q8KC80 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KC80 Go to UniProtKB: Q8KC80
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KC80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC (Subject of Investigation/LOI) Query on APC Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], N [auth C], S [auth D]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D]
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B], O [auth C], T [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B], R [auth C], W [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] P [auth C] Q [auth C] U [auth D] G [auth A], H [auth A], P [auth C], Q [auth C], U [auth D], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]