4QM1

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor D67

• PDB DOI: https://doi.org/10.2210/pdb4QM1/pdb
• Entry: 4QM1 supersedes: 4MXS

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-14 Released: 2014-07-23 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Mandapati, K., Gollapalli, D., Gorla, S.K., Zhang, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor D67

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 165.78 kDa 
• Atom Count: 10,079 
• Modelled Residue Count: 1,350 
• Deposited Residue Count: 1,536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D	384	Bacillus anthracis	Mutation(s): 0  Gene Names: guaB, BA_0008, BAS0011, GBAA_0008 EC: 1.1.1.205
UniProt
Find proteins for A0A6L8P2U9 (Bacillus anthracis) Explore A0A6L8P2U9  Go to UniProtKB:  A0A6L8P2U9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
39H	F [auth A], H [auth B], I [auth C], J [auth C]	2-(3-methyl-4-oxo-3,4-dihydrophthalazin-1-yl)-N-(6,7,8,9-tetrahydrodibenzo[b,d]furan-2-yl)acetamide C23 H21 N3 O3 GMQDVIPGHXODOQ-UHFFFAOYSA-N
IMP	E [auth A], G [auth B], K [auth C], L [auth D]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
39H	BindingDB:  4QM1	Ki: min: 12, max: 500 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34QM1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.13	α = 90
b = 101.331	β = 109.57
c = 87.267	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

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Mandapati, K., Gollapalli, D., Gorla, S.K., Zhang, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 4MXS

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2014-10-08
  Changes: Structure summary
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description