5URS

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P178

PDB DOI: https://doi.org/10.2210/pdb5URS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-12 Released: 2017-03-08
Deposition Author(s): Kim, Y., Maltseva, N., Makowska-Grzyska, M., Gu, M., Gollapalli, D., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.279
R-Value Work: 0.224
R-Value Observed: 0.226

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P178

Kim, Y., Maltseva, N., Makowska-Grzyska, M., Gu, M., Gollapalli, D., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 333.14 kDa
Atom Count: 21,357
Modelled Residue Count: 2,798
Deposited Residue Count: 3,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	384	Bacillus anthracis	Mutation(s): 0 Gene Names: guaB, GBAA_0008, A8C77_00065, ABW01_29210 EC: 1.1.1.205
UniProt
Find proteins for A0A6L8P2U9 (Bacillus anthracis) Explore A0A6L8P2U9 Go to UniProtKB: A0A6L8P2U9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L8P2U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8LA Query on 8LA Download Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain LA [auth H] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	FA [auth F] IA [auth G] J [auth A] LA [auth H] O [auth B] FA [auth F], IA [auth G], J [auth A], LA [auth H], O [auth B], R [auth C], W [auth D], Z [auth E]	N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea C₂₄ H₂₉ Cl N₂ O₆ DGCHEIBDGDMRPM-YSFYHYPLSA-N		Interactions Focus chain FA [auth F] Focus chain IA [auth G] Focus chain J [auth A] Focus chain LA [auth H] Focus chain O [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain FA [auth F] Focus chain IA [auth G] Focus chain J [auth A] Focus chain LA [auth H] Focus chain O [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain Z [auth E]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain KA [auth H] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	EA [auth F] HA [auth G] I [auth A] KA [auth H] N [auth B] EA [auth F], HA [auth G], I [auth A], KA [auth H], N [auth B], Q [auth C], V [auth D], Y [auth E]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain EA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain KA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain EA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain KA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Y [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain BA [auth E]	BA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Interactions & Density Focus chain BA [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	CA [auth E], S [auth C], T [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth E] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain CA [auth E] Focus chain S [auth C] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D] mmCIF format, chain X [auth D]	X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain X [auth D] Interactions & Density Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth F] SDF format, chain JA [auth G] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C]	AA [auth E] DA [auth E] GA [auth F] JA [auth G] K [auth A] AA [auth E], DA [auth E], GA [auth F], JA [auth G], K [auth A], M [auth A], P [auth B], U [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain K [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain K [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.279
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.345	α = 98.71
b = 89.581	β = 89.82
c = 104.158	γ = 96.69

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2017-04-05
Changes: Structure summary
Version 1.2: 2017-09-20
Changes: Author supporting evidence
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description