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- PDB-6lrj: Human cGAS catalytic domain bound with compound 23 -

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Basic information

Entry
Database: PDB / ID: 6lrj
TitleHuman cGAS catalytic domain bound with compound 23
ComponentsCyclic GMP-AMP synthase
KeywordsDNA BINDING PROTEIN / cGAS / Inhibitor / Complex structure
Function / homology
Function and homology information


water channel activity / plasma membrane
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Beta Polymerase; domain 2 ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EQX / Probable aquaporin AqpM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhao, W.F. / Xiong, M.Y. / Yuan, X.J. / Sun, H.B. / Xu, Y.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81620108027 China
National Natural Science Foundation of China (NSFC)21632008 China
CitationJournal: J.Chem.Inf.Model. / Year: 2020
Title: In Silico Screening-Based Discovery of Novel Inhibitors of Human Cyclic GMP-AMP Synthase: A Cross-Validation Study of Molecular Docking and Experimental Testing.
Authors: Zhao, W. / Xiong, M. / Yuan, X. / Li, M. / Sun, H. / Xu, Y.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2786
Polymers85,5192
Non-polymers7594
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.825, 47.072, 87.020
Angle α, β, γ (deg.)90.000, 113.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cyclic GMP-AMP synthase / h-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 42759.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#2: Chemical ChemComp-EQX / 4-[2-(2-methyl-[1,2,4]triazolo[1,5-c]quinazolin-5-yl)hydrazinyl]-4-oxidanylidene-butanoic acid


Mass: 314.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 18-20% V/V PEG 3350, 0.2M AMMONIUM CITRATE (PH 7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24097 / % possible obs: 96.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 44.74 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.071 / Rrim(I) all: 0.161 / Χ2: 0.769 / Net I/σ(I): 6.5 / Num. measured all: 116042
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.644.81.39111960.630.6951.5620.49798.4
2.64-2.694.81.14112060.8010.5751.2840.48598.4
2.69-2.744.91.01212220.7480.5031.1350.49997.3
2.74-2.84.80.84311690.8080.4220.9470.5496.8
2.8-2.864.70.69911660.8180.3510.7860.53896.4
2.86-2.934.70.65212370.8360.3260.7320.58597.3
2.93-34.30.49711370.9150.260.5650.65393.7
3-3.084.30.42211030.9010.220.480.6990
3.08-3.174.90.36211870.9430.1770.4050.71896
3.17-3.285.20.30512020.9540.1460.340.76698.1
3.28-3.395.30.2412270.9630.1150.2670.84997.8
3.39-3.535.20.21312200.9740.1030.2380.99998.7
3.53-3.6950.17512280.9730.0870.1961.09998.6
3.69-3.885.10.14312360.9730.0710.161.15699
3.88-4.134.90.11512300.9770.0580.1291.03699.1
4.13-4.454.80.09712100.9840.0480.1091.06797.3
4.45-4.894.70.08312210.9860.0430.0940.97197.1
4.89-5.64.50.07712190.9890.0410.0880.81597.3
5.6-7.054.70.07511870.9860.0370.0840.66593.7
7.05-504.80.06512940.9920.0320.0730.60496.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEV

4lev


Resolution: 3→43.509 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 688 4.6 %
Rwork0.2078 14281 -
obs0.2101 14969 91.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.63 Å2 / Biso mean: 43.0855 Å2 / Biso min: 11.65 Å2
Refinement stepCycle: final / Resolution: 3→43.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5211 0 48 1 5260
Biso mean--50.97 26.9 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025359
X-RAY DIFFRACTIONf_angle_d0.5167219
X-RAY DIFFRACTIONf_chiral_restr0.038811
X-RAY DIFFRACTIONf_plane_restr0.003905
X-RAY DIFFRACTIONf_dihedral_angle_d2.3163252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.23160.36461230.2729216771
3.2316-3.55670.28651300.2176295795
3.5567-4.0710.25791490.2026304098
4.071-5.12780.23141550.1817303997
5.1278-43.5090.23571310.2098307895
Refinement TLS params.Method: refined / Origin x: 20.2275 Å / Origin y: -10.1544 Å / Origin z: 23.2249 Å
111213212223313233
T0.1758 Å20.0036 Å2-0.0287 Å2-0.1583 Å2-0.0142 Å2--0.1784 Å2
L0.498 °2-0.2065 °2-0.3641 °2-0.4419 °20.2041 °2--0.6402 °2
S0.0189 Å °0.1133 Å °-0.0401 Å °-0.09 Å °-0.0522 Å °0.098 Å °-0.0487 Å °-0.1368 Å °0.0141 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA162 - 519
2X-RAY DIFFRACTION1allB161 - 519
3X-RAY DIFFRACTION1allD1 - 2
4X-RAY DIFFRACTION1allE1 - 2
5X-RAY DIFFRACTION1allS1

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