7FTQ | pdb_00007ftq

Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-5-fluoro-4-methylphenyl)-1H-benzimidazole-4-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb7FTQ/pdb
Deposition Group: G_1002263 | Explore G_1002263

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-08 Released: 2024-02-21
Deposition Author(s): Leibrock, L., Benz, J., Groebke-Zbinden, K., Zhou, C., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.213 (Depositor), 0.218 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of a human cyclic GMP-AMP synthase complex

Groebke-Zbinden, K., Vandemeulebroucke, A., Hilbert, M., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 42.87 kDa
Atom Count: 2,982
Modeled Residue Count: 353
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	A	362	Homo sapiens	Mutation(s): 0 Gene Names: CGAS, C6orf150, MB21D1 EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N884 (Homo sapiens) Explore Q8N884 Go to UniProtKB: Q8N884
PHAROS: Q8N884 GTEx: ENSG00000164430
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N884
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YM9 (Subject of Investigation/LOI) Query on YM9 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(5M)-5-(2-chloro-5-fluoro-4-methylphenyl)-1H-benzimidazole-7-carboxylic acid C₁₅ H₁₀ Cl F N₂ O₂ DYYWPYAEACAPSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.213 (Depositor), 0.218 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.28	α = 90
b = 47.71	β = 90
c = 59.8	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Groebke-Zbinden, K.

Funding Organization	Location	Grant Number
F. Hoffmann-La Roche LTD	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2024-02-21
Type: Initial release
Version 1.1: 2026-02-18
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.