4MY1

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Bacillus anthracis str. Ames complexed with P68

• PDB DOI: https://doi.org/10.2210/pdb4MY1/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Bacillus anthracis str. Ames
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-26 Released: 2014-01-01 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Gorla, S.K., 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: 2.60 Å
• R-Value Free: 0.253 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Bacillus anthracis str. Ames complexed with P68

Kim, Y., Makowska-Grzyska, M., Gu, M., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 331.58 kDa 
• Atom Count: 21,010 
• Modelled Residue Count: 2,798 
• Deposited Residue Count: 3,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D, E, F, G, H	384	Bacillus anthracis str. Ames	Mutation(s): 0  Gene Names: BAS0011, BA_0008, GBAA_0008, guaB 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
P68	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], S [auth E], V [auth G], X [auth H]	1-(4-bromophenyl)-3-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea C18 H20 Br N3 O2 DSTKQECXQMKQLN-WSDLNYQXSA-N
IMP	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], T [auth F], U [auth G], W [auth H]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P68	BindingDB:  4MY1	Ki: min: 2.3, max: 48 (nM) from 2 assay(s)
		IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.253 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M34MY1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.22	α = 81.13
b = 89.391	β = 89.95
c = 103.987	γ = 83.59

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: 2014-01-01 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-01-01
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description