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- PDB-5uwx: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 5uwx
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P176
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
Keywordsoxidoreductase/oxidoreductase inhibitor / TIM barrel / IMPDH / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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-8L7 / ACETIC ACID / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMaltseva, N. / Kim, Y. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D.R. / Hedstrom, L. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding.
Authors: Wang, X. / Rosenberg, M.M. / Kim, Y. / Maltseva, N. / Cuny, G.D. / Joachimiak, A. / Kuzmic, P. / Hedstrom, L.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / diffrn_detector / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation_author.name / _diffrn_detector.detector / _pdbx_struct_assembly_prop.value
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Mar 25, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,83320
Polymers153,7654
Non-polymers4,06816
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-80 kcal/mol
Surface area58960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.278, 118.943, 96.992
Angle α, β, γ (deg.)90.00, 102.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH


Mass: 38441.266 Da / Num. of mol.: 4
Mutation: CBS domain (residues 89-215) is replaced with SGG residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: guaB_2, guaB, ERS852446_02285, JFP838_13815 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A127ELD1, IMP dehydrogenase

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Non-polymers , 6 types, 493 molecules

#2: Chemical
ChemComp-8L7 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-alpha-D-ribofuranosylamine


Mass: 475.965 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30ClN3O5
#3: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 47.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium acetate, 0.1M Bis-Tris pH 6.5, 45% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2016 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→47.5 Å / Num. obs: 118158 / % possible obs: 97.5 % / Redundancy: 5.9 % / Rsym value: 0.096 / Net I/σ(I): 16.34
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.79 / Num. unique obs: 5833 / CC1/2: 0.804 / Rsym value: 0.705 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.5 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.197 5793 4.9 %
Rwork0.1625 --
obs0.1642 118136 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10131 0 276 477 10884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810693
X-RAY DIFFRACTIONf_angle_d1.02114481
X-RAY DIFFRACTIONf_dihedral_angle_d22.0133988
X-RAY DIFFRACTIONf_chiral_restr0.0641682
X-RAY DIFFRACTIONf_plane_restr0.0051846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8459-1.86680.31981930.28113455X-RAY DIFFRACTION90
1.8668-1.88880.3191990.27153702X-RAY DIFFRACTION96
1.8888-1.91180.28391810.23853602X-RAY DIFFRACTION94
1.9118-1.9360.26741840.23623727X-RAY DIFFRACTION97
1.936-1.96150.24981740.21073772X-RAY DIFFRACTION97
1.9615-1.98840.22321810.20013755X-RAY DIFFRACTION97
1.9884-2.01680.22762150.19153730X-RAY DIFFRACTION97
2.0168-2.04690.24051910.18813689X-RAY DIFFRACTION97
2.0469-2.07890.23642010.18163749X-RAY DIFFRACTION97
2.0789-2.1130.20951930.1713736X-RAY DIFFRACTION98
2.113-2.14940.2131820.17273788X-RAY DIFFRACTION98
2.1494-2.18850.21911920.16853772X-RAY DIFFRACTION98
2.1885-2.23060.2011830.17153745X-RAY DIFFRACTION98
2.2306-2.27610.20742020.16173688X-RAY DIFFRACTION97
2.2761-2.32560.17751800.15853656X-RAY DIFFRACTION95
2.3256-2.37970.21551910.15933787X-RAY DIFFRACTION98
2.3797-2.43920.19072170.15983764X-RAY DIFFRACTION98
2.4392-2.50520.1982080.15843752X-RAY DIFFRACTION98
2.5052-2.57890.20711900.15773790X-RAY DIFFRACTION98
2.5789-2.66210.22030.15743783X-RAY DIFFRACTION98
2.6621-2.75720.20421970.1683788X-RAY DIFFRACTION98
2.7572-2.86760.19832010.16573753X-RAY DIFFRACTION98
2.8676-2.99810.21531840.17383664X-RAY DIFFRACTION94
2.9981-3.15610.19332010.16783783X-RAY DIFFRACTION99
3.1561-3.35380.22291890.16473842X-RAY DIFFRACTION99
3.3538-3.61270.19062250.15963800X-RAY DIFFRACTION99
3.6127-3.97610.16742000.14793809X-RAY DIFFRACTION99
3.9761-4.5510.16671470.1353759X-RAY DIFFRACTION96
4.551-5.73230.18181970.14943869X-RAY DIFFRACTION99
5.7323-47.52190.17861920.15943834X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / 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)
13.5618-0.0453-0.88260.42710.48991.79990.1144-0.26750.08070.1711-0.0971-0.1046-0.31780.0149-0.03520.3538-0.05140.03610.23130.01880.23163.98613.508538.3743
21.13880.1657-0.12871.1343-0.06120.69910.1139-0.1959-0.14460.1638-0.0778-0.3022-0.12810.2372-0.03710.302-0.1074-0.01750.32610.01540.346421.6688-3.451237.4188
32.4445-0.7181-0.81891.52570.44871.33650.12590.2024-0.0471-0.1625-0.0831-0.1845-0.20330.1062-0.05990.3218-0.08330.03440.30780.00680.328916.26760.069721.3775
43.18581.36540.33833.13470.14682.85160.0879-0.00230.1439-0.0269-0.1041-0.0407-0.1017-0.13160.01220.29620.06990.05780.1890.02370.3-2.05045.538426.7911
54.20980.19142.40163.68720.56423.58820.0468-0.4224-0.49030.1342-0.1614-0.1105-0.0982-0.05420.06820.2028-0.04560.01530.24530.08420.2439-1.0475-21.455337.1732
61.11940.0265-0.12632.05960.49562.0461-0.03060.027-0.6449-0.10180.051-0.6530.19230.1981-0.02150.2690.05940.06910.30870.01840.76089.2701-45.961125.5199
76.1022-2.5486-0.12451.18-0.58693.25610.02360.3224-0.9009-0.1262-0.1248-0.24410.6654-0.04230.07610.34370.03740.06080.2789-0.02890.7373-0.878-55.495625.2713
83.8705-4.20930.46374.5623-0.44892.0664-0.00350.0012-0.6409-0.0918-0.0709-0.23760.447-0.03590.06080.2838-0.03340.00740.237-0.00490.611-6.9709-51.249531.2598
91.99030.53540.3361.6738-0.03611.3476-0.05860.0181-0.3688-0.06580.009-0.42960.06660.08720.04960.17240.00960.03220.194-0.0020.3881-0.8558-36.03127.4988
106.4662-1.2022-2.11193.51950.38394.5202-0.24930.6977-0.7669-0.35370.0396-0.03110.3201-0.34190.18310.354-0.03380.1020.3445-0.11590.3403-2.8067-38.152511.7767
112.3835-0.63260.12172.77050.73241.31480.0826-0.1624-0.25060.1178-0.0461-0.47810.00640.1787-0.03650.2127-0.0587-0.02240.29370.07180.40919.4198-24.078434.1538
125.5659-3.2403-2.28683.1752-0.82964.51780.03750.4481-0.606-0.7147-0.09910.2919-0.0796-0.01420.09660.3482-0.04440.0150.3539-0.02760.416312.2001-14.895718.0624
131.29510.27650.01662.29050.3251.18320.0230.0446-0.0575-0.075-0.0484-0.126-0.17230.11970.13330.2172-0.0335-0.00950.2988-0.01480.244622.4255-19.8722-31.2159
142.6370.32650.67321.17180.45342.77390.2438-0.6628-0.22090.4913-0.2585-0.49090.08590.4216-0.03630.3629-0.0534-0.14090.6150.15230.395741.9606-26.6003-9.0723
154.7588-3.46822.39553.3819-1.83281.84510.0191-0.22360.03560.1468-0.0547-0.2926-0.06640.26910.05770.2648-0.1268-0.08160.5770.04410.400347.9706-16.0088-17.849
161.67830.13530.11141.869-0.07460.50070.1075-0.09960.04070.0216-0.0964-0.2932-0.08620.2859-0.02650.1949-0.0403-0.01620.37620.01830.257134.378-18.7301-23.1271
171.38660.6515-0.17752.73040.69911.62550.2152-0.6267-0.01450.7244-0.29640.0234-0.02090.24330.08180.3837-0.1153-0.03280.5330.03870.25525.7981-23.6117-5.9205
184.3782-0.7346-1.26322.674-0.71752.64740.0361-0.1361-0.15790.2191-0.04110.0894-0.099-0.019-0.00740.1972-0.0415-0.0470.2283-0.03640.237914.9421-28.992-21.6246
199.04482.32971.68013.17480.73542.94880.3022-0.00510.28490.097-0.23850.0658-0.2345-0.1408-0.04190.2950.05030.05460.22080.03320.177541.1953-61.819929.4916
202.17-0.0634-0.82412.4852-0.23271.93490.0440.24160.57-0.34020.06110.3039-0.805-0.307-0.06940.81180.26570.05870.43010.18650.536540.5252-37.075915.2923
212.5384-2.45460.70483.6493-2.42562.58860.61630.2480.89040.1546-0.3168-0.2982-0.8198-0.0694-0.1070.93860.14010.15880.37270.12840.627248.6202-26.715621.956
223.4327-3.20210.87824.4472-1.81790.88180.093-0.03730.65470.1031-0.0472-0.0693-0.7135-0.22540.02650.76510.08630.12820.25320.01250.412449.3681-32.206229.8853
233.7093-2.87631.34932.6354-1.1060.5043-0.0993-0.46020.43750.4850.0920.0392-0.8155-0.3541-0.03150.67650.15690.09780.3603-0.00260.424245.7251-37.313734.1809
241.49160.61590.2311.1390.21730.7280.0367-0.04360.15120.07040.03380.1445-0.3826-0.1845-0.0770.42440.12170.06590.28710.05990.288246.7203-50.286327.7594
251.14121.1906-0.2711.3799-1.02584.41170.05550.50020.1147-0.37070.17310.0761-0.5979-0.1968-0.25710.53870.07750.02640.37340.11730.347649.5484-47.80877.2948
268.85081.34155.42872.23041.03973.37870.12550.48510.0566-0.20730.0609-0.1515-0.48140.1046-0.07570.5802-0.01180.12680.42530.09090.294457.6185-45.552311.1967
274.0493.4252-3.94333.5611-2.99143.9871-0.04980.4182-0.0753-0.5634-0.3512-0.1614-0.0009-0.10760.26750.42710.2106-0.02440.49080.12820.37733.2268-54.503813.7618
282.09050.09971.0743.0505-0.00884.1180.08840.33040.2415-0.2387-0.11590.1551-0.2713-0.17480.01370.25770.07550.03320.31370.09630.287639.056-63.865519.0155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 350 )
3X-RAY DIFFRACTION3chain 'A' and (resid 351 through 441 )
4X-RAY DIFFRACTION4chain 'A' and (resid 442 through 481 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 89 )
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 237 )
8X-RAY DIFFRACTION8chain 'B' and (resid 238 through 265 )
9X-RAY DIFFRACTION9chain 'B' and (resid 266 through 384 )
10X-RAY DIFFRACTION10chain 'B' and (resid 385 through 422 )
11X-RAY DIFFRACTION11chain 'B' and (resid 423 through 466 )
12X-RAY DIFFRACTION12chain 'B' and (resid 467 through 482 )
13X-RAY DIFFRACTION13chain 'C' and (resid -2 through 24 )
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 237 )
15X-RAY DIFFRACTION15chain 'C' and (resid 238 through 265 )
16X-RAY DIFFRACTION16chain 'C' and (resid 266 through 350 )
17X-RAY DIFFRACTION17chain 'C' and (resid 351 through 440 )
18X-RAY DIFFRACTION18chain 'C' and (resid 441 through 482 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 24 )
20X-RAY DIFFRACTION20chain 'D' and (resid 25 through 89 )
21X-RAY DIFFRACTION21chain 'D' and (resid 90 through 237 )
22X-RAY DIFFRACTION22chain 'D' and (resid 238 through 265 )
23X-RAY DIFFRACTION23chain 'D' and (resid 266 through 288 )
24X-RAY DIFFRACTION24chain 'D' and (resid 289 through 350 )
25X-RAY DIFFRACTION25chain 'D' and (resid 351 through 384 )
26X-RAY DIFFRACTION26chain 'D' and (resid 385 through 422 )
27X-RAY DIFFRACTION27chain 'D' and (resid 423 through 441 )
28X-RAY DIFFRACTION28chain 'D' and (resid 442 through 481 )

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