[English] 日本語
Yorodumi
- PDB-9ntk: Chimeric Adenosine deaminase growth factor (ADGF) in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ntk
TitleChimeric Adenosine deaminase growth factor (ADGF) in complex with pentostatin monophosphate
ComponentsAdenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
KeywordsHYDROLASE / Chimeric Adenosine deaminase growth factor (ADGF) apoenzyme / Adenosine deaminase / Pentostatin mono phosphate / Deoxycoformycin 5' phosphate
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / adenosine deaminase activity / adenosine catabolic process / extracellular space / metal ion binding
Similarity search - Function
Adenosine deaminase-related growth factor / Adenosine/AMP deaminase N-terminal / Adenosine/AMP deaminase N-terminal / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
: / Adenosine deaminase AGSA
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsKaur, G. / Horton, J.R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural basis for the substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase.
Authors: Kaur, G. / Horton, J.R. / Tzertzinis, G. / Zhou, J. / Schildkraut, I. / Cheng, X.
History
DepositionMar 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 23, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
B: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
C: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
D: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,07446
Polymers245,5334
Non-polymers8,54142
Water2,126118
1
A: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
B: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,09924
Polymers122,7662
Non-polymers4,33322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
D: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97522
Polymers122,7662
Non-polymers4,20920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.834, 118.477, 109.546
Angle α, β, γ (deg.)90.000, 98.488, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 28 - 521 / Label seq-ID: 28 - 521

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.999994670135, 0.00316939766919, -0.000783976894721), (0.00314250597446, 0.999476315316, 0.0322058966442), (0.000885639631787, 0.0322032613391, -0.999480948093)-35.4921386892, 0.0721610717602, -0.0859734303836
2given(-0.957267258066, -0.012767255718, -0.288922816365), (0.0111395285548, -0.999911470941, 0.00727744355926), (-0.288990151283, 0.00374799447867, 0.957324733306)-42.9118814073, -25.1870139195, 49.0710464228
3given(0.956617454718, -0.0129961973277, 0.291056943199), (-0.00278608654573, -0.999366984579, -0.0354664327912), (0.291333628424, 0.0331168988312, -0.956048109648)-8.74869676925, -25.4164472743, 59.3494275229

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor / Atrial gland-specific antigen / AGSA / Mollusk-derived growth factor / MDGF


Mass: 61383.203 Da / Num. of mol.: 4 / Fragment: residues 1-120,residues 254-525
Source method: isolated from a genetically manipulated source
Details: residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA,residues 1-120 of A. ...Details: residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA,residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA,residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Komagataella pastoris (fungus) / References: UniProt: P15287, adenosine deaminase

-
Sugars , 2 types, 16 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 144 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-A1CDW / pentostatin 5'-phosphate / (8S)-3-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol / 2'-deoxycoformycin 5'-phosphate


Mass: 348.249 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H17N4O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.53→29.63 Å / Num. obs: 76443 / % possible obs: 97.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 37.72 Å2 / CC1/2: 0.96 / Rpim(I) all: 0.163 / Net I/σ(I): 4.6
Reflection shellResolution: 2.53→2.59 Å / Redundancy: 2.5 % / Num. unique obs: 5236 / CC1/2: 0.372 / Rpim(I) all: 0.985

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→29.63 Å / SU ML: 0.4046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 1998 2.62 %
Rwork0.2116 74358 -
obs0.2127 76356 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.35 Å2
Refinement stepCycle: LAST / Resolution: 2.53→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15960 0 544 118 16622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005716886
X-RAY DIFFRACTIONf_angle_d0.879522904
X-RAY DIFFRACTIONf_chiral_restr0.05122596
X-RAY DIFFRACTIONf_plane_restr0.00682896
X-RAY DIFFRACTIONf_dihedral_angle_d15.04176578
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.5420677995
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.604458811636
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.619541079966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.590.34011310.32254907X-RAY DIFFRACTION89.92
2.59-2.660.33961450.29815361X-RAY DIFFRACTION98.48
2.66-2.740.34711440.28025375X-RAY DIFFRACTION98.26
2.74-2.830.36241440.27825348X-RAY DIFFRACTION98.25
2.83-2.930.31671420.2715296X-RAY DIFFRACTION98.21
2.93-3.040.32231450.26845363X-RAY DIFFRACTION98.2
3.04-3.180.3181450.24485388X-RAY DIFFRACTION98.56
3.18-3.350.25821450.22265380X-RAY DIFFRACTION98.41
3.35-3.560.24771430.20925322X-RAY DIFFRACTION97.92
3.56-3.830.27971430.19265342X-RAY DIFFRACTION97.49
3.83-4.220.19721430.1695346X-RAY DIFFRACTION97.43
4.22-4.830.16851440.14735295X-RAY DIFFRACTION97
4.83-6.070.24561430.16985337X-RAY DIFFRACTION96.7
6.07-29.630.17131410.16585298X-RAY DIFFRACTION94.95

+
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