[English] 日本語
Yorodumi
- PDB-5uzc: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uzc
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P221
ComponentsInosine-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-8N1 / ACETIC ACID / FORMIC 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)
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 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,80721
Polymers153,7654
Non-polymers4,04217
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23320 Å2
ΔGint-189 kcal/mol
Surface area46450 Å2
2
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)315,61342
Polymers307,5308
Non-polymers8,08334
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area50110 Å2
ΔGint-383 kcal/mol
Surface area89440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.017, 119.305, 97.199
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

21A-722-

HOH

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
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 (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria)
Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A
Gene: guaB, CPF_2558 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A0A0H2YRZ7, IMP dehydrogenase

-
Non-polymers , 7 types, 426 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-8N1 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-xylofuranosylamine


Mass: 475.965 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30ClN3O5
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M ammonium acetate, 0.1M Tris pH 8.5, 45% MPD

-
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 25, 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→50 Å / Num. obs: 120850 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 34.84 Å2 / Rsym value: 0.107 / Net I/σ(I): 15.05
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5984 / CC1/2: 0.67 / Rsym value: 0.797 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q32

4q32


Resolution: 1.85→44.513 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.08
RfactorNum. reflection% reflection
Rfree0.2007 5934 4.91 %
Rwork0.1708 --
obs0.1723 120807 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10143 0 274 409 10826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110805
X-RAY DIFFRACTIONf_angle_d1.20814643
X-RAY DIFFRACTIONf_dihedral_angle_d23.2174022
X-RAY DIFFRACTIONf_chiral_restr0.0731689
X-RAY DIFFRACTIONf_plane_restr0.0061866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.846-1.86690.34582000.32063609X-RAY DIFFRACTION93
1.8669-1.88890.31511850.30423749X-RAY DIFFRACTION99
1.8889-1.91190.33231990.28023833X-RAY DIFFRACTION99
1.9119-1.93610.29971940.27863831X-RAY DIFFRACTION99
1.9361-1.96160.27261810.25373844X-RAY DIFFRACTION99
1.9616-1.98850.2591850.24273845X-RAY DIFFRACTION99
1.9885-2.01690.25852180.23513772X-RAY DIFFRACTION99
2.0169-2.0470.25931910.22833767X-RAY DIFFRACTION98
2.047-2.0790.25712050.21293868X-RAY DIFFRACTION99
2.079-2.11310.25062050.20573818X-RAY DIFFRACTION100
2.1131-2.14950.23281830.20263822X-RAY DIFFRACTION100
2.1495-2.18860.21451970.19133885X-RAY DIFFRACTION100
2.1886-2.23070.22831950.18883801X-RAY DIFFRACTION100
2.2307-2.27620.22351920.17673861X-RAY DIFFRACTION99
2.2762-2.32570.2132010.18183835X-RAY DIFFRACTION100
2.3257-2.37980.19261940.1783866X-RAY DIFFRACTION99
2.3798-2.43930.20912150.17633819X-RAY DIFFRACTION99
2.4393-2.50530.20222120.17193762X-RAY DIFFRACTION98
2.5053-2.5790.21281890.17083859X-RAY DIFFRACTION100
2.579-2.66220.20492170.16953841X-RAY DIFFRACTION100
2.6622-2.75740.18551940.17823830X-RAY DIFFRACTION100
2.7574-2.86770.21162030.17733832X-RAY DIFFRACTION100
2.8677-2.99820.21722020.18093900X-RAY DIFFRACTION100
2.9982-3.15630.18932040.17373808X-RAY DIFFRACTION99
3.1563-3.3540.21681890.17123850X-RAY DIFFRACTION99
3.354-3.61280.1852300.15943823X-RAY DIFFRACTION100
3.6128-3.97620.16881990.1483868X-RAY DIFFRACTION100
3.9762-4.5510.1661600.13613897X-RAY DIFFRACTION99
4.551-5.73190.18621980.14983862X-RAY DIFFRACTION99
5.7319-44.52560.17781970.15273916X-RAY DIFFRACTION99
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)
11.46060.22910.24881.5228-0.14131.35540.03510.13350.1406-0.09690.07310.1097-0.2953-0.0733-0.10930.37690.07810.02640.26380.05560.311-16.31229.117720.0885
21.25510.2535-0.43660.8726-0.76962.5851-0.03770.37890.1228-0.21250.06490.0633-0.29780.0118-0.04180.47580.11470.02010.31970.03710.3768-16.653929.176512.5303
33.2875-0.35240.66843.3527-0.17645.59340.07380.33620.2461-0.2025-0.04090.1067-0.2295-0.0217-0.06680.19930.0128-0.00880.23680.0660.2713-25.110614.535218.9674
41.4006-0.4820.46867.5564-0.69920.8911-0.082-0.0584-0.14520.18920.0070.2273-0.0759-0.10260.07670.20110.0171-0.00990.3040.00620.2732-21.7884-2.577831.2378
52.0954-0.60730.37021.6902-1.10742.3640.18960.545-0.3822-0.3426-0.11260.27680.1499-0.2034-0.08170.36130.0215-0.12290.5509-0.15770.4123-39.1725-9.7439.1552
63.00770.47110.38271.63120.37731.28770.06520.1543-0.0194-0.1314-0.12330.395-0.0161-0.39620.06030.23910.0664-0.04020.4557-0.03660.3763-42.26261.752519.1882
71.227-0.9396-0.05982.5467-0.8711.96660.19790.5424-0.1189-0.5669-0.26790.0179-0.0254-0.11230.05170.33310.0561-0.05760.4648-0.06850.2731-26.0819-5.00448.9756
83.16790.4753-0.5173.16620.42092.68940.050.1585-0.1605-0.1951-0.0217-0.0541-0.1039-0.01-0.03580.21820.0386-0.0590.25530.01170.3018-14.4569-9.499721.7287
95.14970.64361.22693.76990.20853.40140.1391-0.33-0.44060.0721-0.1382-0.0564-0.0175-0.16080.02930.2021-0.03970.01740.21090.04870.2281-0.3605-2.441537.2974
101.6950.1913-0.05331.4223-0.03960.9653-0.03150.0479-0.4252-0.0709-0.0055-0.29880.16770.09870.0390.22280.01520.00490.2444-0.010.45311.4586-23.679127.3636
113.62810.0120.09352.15671.89294.14830.09450.5353-0.5062-0.14140.0296-0.40060.1210.1925-0.1960.28840.01490.04450.19180.06710.42415.0078-15.260619.0381
123.226-0.0461-0.93733.3282-0.74752.37660.05530.1677-0.0843-0.0328-0.033-0.2213-0.2250.002-0.00190.1876-0.0622-0.04590.2373-0.0260.30047.58680.693629.7048
133.36990.6517-1.6070.2317-0.62972.8552-0.1756-0.2636-0.46890.1371-0.00540.09630.0562-0.13290.15330.281-0.00320.02960.31530.03940.2579-5.548715.638138.4632
141.26170.0785-0.22761.1745-0.06330.840.0917-0.0753-0.02560.0738-0.0655-0.2272-0.11770.1725-0.02510.2849-0.0822-0.00530.30010.00490.350319.672317.902632.9524
153.34651.14620.322.8365-0.00011.68380.02850.02310.1305-0.094-0.095-0.0744-0.1641-0.13960.05710.28170.04310.0480.1710.01310.2678-1.998324.381626.5503
160.88690.8599-0.72043.2311-0.9011.50.11940.23510.4692-0.16140.04310.2612-0.5476-0.2155-0.17720.52540.13610.04350.35240.08130.3998-22.528236.564419.0906
174.1188-2.51262.6623.1252-2.83423.36250.14170.19720.8749-0.0595-0.295-0.1206-0.4711-0.03630.17380.70580.11020.12990.27930.03910.508-15.519548.472424.7292
183.9009-2.46360.67149.2022-0.96171.80160.0522-0.27170.33020.34680.13160.2182-0.71-0.192-0.17210.60540.07340.12010.2897-0.01870.3301-16.902444.133734.2871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 289 through 384 )
2X-RAY DIFFRACTION2chain 'C' and (resid 385 through 441 )
3X-RAY DIFFRACTION3chain 'C' and (resid 442 through 481 )
4X-RAY DIFFRACTION4chain 'D' and (resid -1 through 24 )
5X-RAY DIFFRACTION5chain 'D' and (resid 25 through 88 )
6X-RAY DIFFRACTION6chain 'D' and (resid 89 through 329 )
7X-RAY DIFFRACTION7chain 'D' and (resid 330 through 440 )
8X-RAY DIFFRACTION8chain 'D' and (resid 441 through 482 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 24 )
10X-RAY DIFFRACTION10chain 'A' and (resid 25 through 384 )
11X-RAY DIFFRACTION11chain 'A' and (resid 385 through 440 )
12X-RAY DIFFRACTION12chain 'A' and (resid 441 through 482 )
13X-RAY DIFFRACTION13chain 'B' and (resid -2 through 24 )
14X-RAY DIFFRACTION14chain 'B' and (resid 25 through 441 )
15X-RAY DIFFRACTION15chain 'B' and (resid 442 through 482 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 227 )
17X-RAY DIFFRACTION17chain 'C' and (resid 228 through 252 )
18X-RAY DIFFRACTION18chain 'C' and (resid 253 through 288 )

+
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