4Q32 | pdb_00004q32

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and C91

PDB DOI: https://doi.org/10.2210/pdb4Q32/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium perfringens ATCC 13124
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-04-10 Released: 2014-07-09
Deposition Author(s): Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Gu, M., Zhang, M., Mandapati, K., Gollapalli, D.R., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and C91

Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Gu, M., Zhang, M., Mandapati, K., Gollapalli, D.R., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 156.67 kDa
Atom Count: 10,326
Modelled Residue Count: 1,358
Deposited Residue Count: 1,452
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D	363	Clostridium perfringens ATCC 13124	Mutation(s): 0 Gene Names: CPF_2558, guaB EC: 1.1.1.205
UniProt
Find proteins for A0A0H2YRZ7 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YRZ7 Go to UniProtKB: A0A0H2YRZ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2YRZ7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C91 Query on C91 Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	F [auth A], G [auth A], I [auth B], K [auth D]	N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide C₂₄ H₁₈ N₄ O XYCMWFINXXFAFG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth D]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C], L [auth D]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34q32

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.611	α = 90
b = 77.611	β = 90
c = 222.726	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2017-07-26
Changes: Refinement description, Source and taxonomy
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and C91

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and C91

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

4Q32 | pdb_00004q32