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- PDB-9ntj: Chimeric Adenosine deaminase growth factor (ADGF) in complex with... -

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Basic information

Entry
Database: PDB / ID: 9ntj
TitleChimeric Adenosine deaminase growth factor (ADGF) in complex with pentostatin
ComponentsAdenosine deaminase AGSA,Adenosine deaminase AGSA,AMP deaminase
KeywordsHYDROLASE / Chimeric Adenosine deaminase growth factor (ADGF) apoenzyme / Adenosine deaminase / Pentostatin / 2'-deoxycoformycin
Function / homology
Function and homology information


2'-deoxyadenosine deaminase activity / inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / 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
2'-DEOXYCOFORMYCIN / Adenosine deaminase AGSA
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Helix pomatia (Roman snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 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 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine deaminase AGSA,Adenosine deaminase AGSA,AMP deaminase
B: Adenosine deaminase AGSA,Adenosine deaminase AGSA,AMP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,10320
Polymers122,7662
Non-polymers3,33718
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-41 kcal/mol
Surface area37500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.349, 109.609, 171.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 61383.203 Da / Num. of mol.: 2 / 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), (gene. exp.) Helix pomatia (Roman snail)
Production host: Komagataella pastoris (fungus) / References: UniProt: P15287, adenosine deaminase

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Sugars , 2 types, 8 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.: 1
Source method: isolated from a genetically manipulated source
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
#3: 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.: 7
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

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Non-polymers , 4 types, 89 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-DCF / 2'-DEOXYCOFORMYCIN


Mass: 268.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticancer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 25% w/v Polyethylene glycol 1,500, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.28→47.69 Å / Num. obs: 18753 / % possible obs: 93.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.803 / Rpim(I) all: 0.123 / Net I/σ(I): 3.1
Reflection shellResolution: 3.29→3.41 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1881 / CC1/2: 0.331 / Rpim(I) all: 0.622

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→47.69 Å / SU ML: 0.4102 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2608 934 5 %
Rwork0.2099 17735 -
obs0.2125 18669 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.23 Å2
Refinement stepCycle: LAST / Resolution: 3.28→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7980 0 212 82 8274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028386
X-RAY DIFFRACTIONf_angle_d0.521911377
X-RAY DIFFRACTIONf_chiral_restr0.04121283
X-RAY DIFFRACTIONf_plane_restr0.00371447
X-RAY DIFFRACTIONf_dihedral_angle_d12.03153240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.450.34831280.28082433X-RAY DIFFRACTION91.4
3.45-3.670.2781350.24562557X-RAY DIFFRACTION95.16
3.67-3.950.31291340.23052548X-RAY DIFFRACTION94.2
3.95-4.350.25761330.19212530X-RAY DIFFRACTION93.9
4.35-4.980.23641290.16572449X-RAY DIFFRACTION89.7
4.98-6.270.23481360.2072582X-RAY DIFFRACTION94.24
6.27-47.690.19851390.17812636X-RAY DIFFRACTION91.1

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