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- PDB-1nf7: Ternary complex of the human type II Inosine Monophosphate Dedhyd... -

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Basic information

Entry
Database: PDB / ID: 1nf7
TitleTernary complex of the human type II Inosine Monophosphate Dedhydrogenase with Ribavirin Monophosphate and C2-Mycophenolic Adenine Dinucleotide
ComponentsInosine-5'-monophosphate dehydrogenase 2
KeywordsOXIDOREDUCTASE / 8 STRANDED PARALLE ALPHA/BETA BARREL / DEHYDROGENASE / IMPD / IMPDH / RIBAVIRIN MONOPHOSPHATE / C2-MAD
Function / homology
Function and homology information


'de novo' XMP biosynthetic process / lymphocyte proliferation / Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / peroxisomal membrane / GTP biosynthetic process / cellular response to interleukin-4 ...'de novo' XMP biosynthetic process / lymphocyte proliferation / Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / peroxisomal membrane / GTP biosynthetic process / cellular response to interleukin-4 / circadian rhythm / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular exosome / extracellular region / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Chem-MYD / RIBAVIRIN MONOPHOSPHATE / UNKNOWN / Inosine-5'-monophosphate dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRisal, D. / Strickler, M.D. / Goldstein, B.M.
CitationJournal: To be Published
Title: Crystal Structure of Human Inosine Monophosphate Dehydrogenase type II complexed with the MPA/NAD analog C2-MAD
Authors: Risal, D. / Strickler, M.D. / Goldstein, B.M.
History
DepositionDec 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase 2
B: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,90219
Polymers111,7502
Non-polymers3,15217
Water1,67593
1
A: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,53416
Polymers223,4994
Non-polymers4,03512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
2
B: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,07260
Polymers223,4994
Non-polymers8,57256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)146.580, 146.580, 128.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inosine-5'-monophosphate dehydrogenase 2 / IMP dehydrogenase 2 / IMPDH-II / IMPD 2


Mass: 55874.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IMPDH2 / Plasmid: pET12B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12268, IMP dehydrogenase

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Non-polymers , 5 types, 110 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-RVP / RIBAVIRIN MONOPHOSPHATE


Mass: 324.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N4O8P
#4: Chemical ChemComp-MYD / {[5-(6-AMINO-PURIN-7-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-[2-(4-HYDROXY-6-METHOXY-7-METHYL-3-OXO-1,3-DIHYDRO-ISOBENZOFURAN-5-YL)-ETHYL] ESTER / C2-MYCOPHENOLIC ADENINE DINUCLEOTIDE


Mass: 645.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N5O13P2
#5: Chemical
ChemComp-UNK / UNKNOWN


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H9NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 3.48 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6% PEG 6000, 0.1M Tris-HCl, 24mM beta-mercaptoethanol, 1M LiCl, 10% Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002 / Details: mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.65→41.24 Å / Num. all: 39557 / Num. obs: 34951 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 16
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2 / Num. unique all: 2383 / Rsym value: 0.371 / % possible all: 89

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A of PDB ENTRY 1B3O

1b3o


Resolution: 2.65→41.24 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. The residues labelled UNK 801 through 811 represent residues whose electron density is robust enough only to trace the main chain. It is not clear how these atoms ...Details: BULK SOLVENT MODEL USED. The residues labelled UNK 801 through 811 represent residues whose electron density is robust enough only to trace the main chain. It is not clear how these atoms correspond to the sequence assignment. The CA atoms are intended to communicate the fact that there is significant density (visible at 0.6 sigma or lower) in the region of the active site that is very near to the bound cofactor analog and therefore potentially making interactions with the analog.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2534 9.9 %RANDOM
Rwork0.238 ---
all0.296 39557 --
obs0.238 25599 64.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.1117 Å2 / ksol: 0.339281 e/Å3
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.8 Å20 Å20 Å2
2---8.8 Å20 Å2
3---17.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-41.24 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.65→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6880 0 141 93 7114
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it8.81.5
X-RAY DIFFRACTIONc_mcangle_it13.742
X-RAY DIFFRACTIONc_scbond_it10.872
X-RAY DIFFRACTIONc_scangle_it15.862.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 198 9.6 %
Rwork0.329 1861 -
obs-1861 31.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMRMP_C2EXO_PRODRG.TOP
X-RAY DIFFRACTION3ION.PARAMC2MAD_ENDO_VER1_1.TOP
X-RAY DIFFRACTION4C2MAD_ENDO.PARAMION.TOP
X-RAY DIFFRACTION5RMP.PARAM

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