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- PDB-8qch: Human Adenosine deaminase-like protein in complex with compound AT8001 -

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Basic information

Entry
Database: PDB / ID: 8qch
TitleHuman Adenosine deaminase-like protein in complex with compound AT8001
ComponentsAdenosine deaminase-like protein
KeywordsHYDROLASE / complex
Function / homology
Function and homology information


N6-methyl-AMP deaminase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / Abacavir metabolism / inosine biosynthetic process / adenosine deaminase activity / adenosine catabolic process / Purine salvage / nucleotide metabolic process / metal ion binding / cytosol
Similarity search - Function
Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Adenosine deaminase-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.442 Å
AuthorsZimberger, C. / canard, B. / Ferron, F.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005 France
Fondation pour la Recherche Medicale (FRM)Soutien aux equipes France
Citation
Journal: Plos Biol. / Year: 2024
Title: The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution.
Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B.
#1: Journal: Biorxiv / Year: 2024
Title: The activation chain of the broad-spectrum antiviral bemnifosbuvir at atomic resolution
Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B.
History
DepositionAug 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine deaminase-like protein
B: Adenosine deaminase-like protein
C: Adenosine deaminase-like protein
D: Adenosine deaminase-like protein
E: Adenosine deaminase-like protein
F: Adenosine deaminase-like protein
G: Adenosine deaminase-like protein
H: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,19746
Polymers322,5598
Non-polymers5,63838
Water14,718817
1
A: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0536
Polymers40,3201
Non-polymers7335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9575
Polymers40,3201
Non-polymers6374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9575
Polymers40,3201
Non-polymers6374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1697
Polymers40,3201
Non-polymers8496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0636
Polymers40,3201
Non-polymers7435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1497
Polymers40,3201
Non-polymers8296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9675
Polymers40,3201
Non-polymers6474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8845
Polymers40,3201
Non-polymers5644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Adenosine deaminase-like protein
B: Adenosine deaminase-like protein
D: Adenosine deaminase-like protein
hetero molecules

C: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,13523
Polymers161,2804
Non-polymers2,85519
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area9670 Å2
ΔGint-165 kcal/mol
Surface area51500 Å2
MethodPISA
10
E: Adenosine deaminase-like protein
F: Adenosine deaminase-like protein
hetero molecules

G: Adenosine deaminase-like protein
H: Adenosine deaminase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,06223
Polymers161,2804
Non-polymers2,78219
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454x-1/2,-y+1/2,-z-11
Buried area9910 Å2
ΔGint-155 kcal/mol
Surface area52270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.757, 142.983, 156.399
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Adenosine deaminase-like protein / Adenosine deaminase-like protein isoform 1 / N6-mAMP deaminase / HsMAPDA / N6-methyl-AMP aminohydrolase


Mass: 40319.891 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAL, ADAL1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6DHV7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines

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Non-polymers , 6 types, 855 molecules

#2: Chemical
ChemComp-EIF / [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate


Mass: 379.238 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H15FN5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2000 mM Ammonium sulfate 100 mM Sodium cacodylate/HCl 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.442→105.752 Å / Num. obs: 119069 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.363 / Rpim(I) all: 0.119 / Rrim(I) all: 0.383 / Net I/σ(I): 7.2
Reflection shellResolution: 2.442→2.484 Å / Redundancy: 10.5 % / Rmerge(I) obs: 3.973 / Mean I/σ(I) obs: 1 / Num. unique obs: 5876 / CC1/2: 0.35 / Rpim(I) all: 1.289 / Rrim(I) all: 4.18 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.442→105.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.494 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.497 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.262
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 5715 -RANDOM
Rwork0.2143 ---
obs0.2157 118763 99.7 %-
Displacement parametersBiso mean: 50.42 Å2
Baniso -1Baniso -2Baniso -3
1--4.7456 Å20 Å20 Å2
2---3.0908 Å20 Å2
3---7.8364 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.442→105.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22068 0 322 817 23207
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00722818HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.930891HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8159SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3906HARMONIC5
X-RAY DIFFRACTIONt_it22818HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2997SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact18738SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion17.55
LS refinement shellResolution: 2.442→2.46 Å
RfactorNum. reflection% reflection
Rfree0.3288 91 -
Rwork0.3175 --
obs--97.82 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1588-0.0095-0.09720.77310.26521.15770.0065-0.07380.1048-0.0738-0.02020.03670.10480.03670.01370.1630.0173-0.0017-0.09490.0184-0.1143-32.866111.8097-20.9249
20.51630.20950.08780.7642-0.36090.9763-0.0991-0.1353-0.0954-0.13530.06180.0062-0.09540.00620.03740.2148-0.0138-0.061-0.1351-0.0055-0.1085-38.008156.0471-21.3175
30.7227-0.08280.27050.5186-0.14440.9657-0.01720.0609-0.07770.06090.0228-0.0911-0.0777-0.0911-0.00560.03680.02370.0374-0.0212-0.0017-0.084515.382247.3365-16.2103
40.76090.170.20310.7060.09270.81090-0.0288-0.043-0.0288-0.04560.1407-0.0430.14070.04560.0271-0.02960.00180.00330.0338-0.0966-15.970543.66216.3465
50.4085-0.15530.24680.9427-0.24421.17310.00570.07750.16440.0775-0.02380.02250.16440.02250.01810.05940.01360.0227-0.0562-0.0077-0.0933-24.836919.3037-60.8298
60.2814-0.41030.09581.27370.11921.1431-0.13410.2023-0.17870.20230.011-0.0001-0.1787-0.00010.12310.0759-0.0016-0.0359-0.07410.0139-0.0785-44.652259.0512-62.5715
70.705-0.283-0.37890.65240.36071.4354-0.0720.039-0.07260.039-0.1192-0.0983-0.0726-0.09830.1912-0.0643-0.01680.00860.0303-0.0633-0.0616.819236.8243-56.6183
81.0256-0.22770.13460.33850.04031.7111-0.0348-0.05980.0346-0.05980.00340.30690.03460.30690.0314-0.1144-0.0010.03470.14830.0711-0.112260.331429.7759-58.517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A12 - 355
2X-RAY DIFFRACTION1{ A|* }A1009
3X-RAY DIFFRACTION2{ B|* }B12 - 355
4X-RAY DIFFRACTION2{ B|* }B1001
5X-RAY DIFFRACTION3{ C|* }C12 - 355
6X-RAY DIFFRACTION3{ C|* }C1010
7X-RAY DIFFRACTION4{ D|* }D10 - 355
8X-RAY DIFFRACTION4{ D|* }D401 - 1002
9X-RAY DIFFRACTION5{ E|* }E12 - 355
10X-RAY DIFFRACTION5{ E|* }E401 - 1008
11X-RAY DIFFRACTION6{ F|* }F12 - 355
12X-RAY DIFFRACTION6{ F|* }F1006
13X-RAY DIFFRACTION7{ G|* }G7 - 355
14X-RAY DIFFRACTION7{ G|* }G401 - 1004
15X-RAY DIFFRACTION8{ H|* }H6 - 355
16X-RAY DIFFRACTION8{ H|* }H1007

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