[English] 日本語
Yorodumi
- PDB-8qch: Human Adenosine deaminase-like protein in complex with compound AT8001 -

+
Open data


ID or keywords:

Loading...

-
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 / inosine biosynthetic process / Abacavir metabolism / adenosine catabolic process / adenosine deaminase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more