4MY9

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor C91

PDB DOI: https://doi.org/10.2210/pdb4MY9/pdb

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

Deposited: 2013-09-27 Released: 2014-06-11
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.216
R-Value Work: 0.170
R-Value Observed: 0.172

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 C91

Kim, Y., Makowska-Grzyska, M., Gu, M., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 332.41 kDa
Atom Count: 21,262
Modelled Residue Count: 2,792
Deposited Residue Count: 3,072
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, E A, B, C, D, E, F, G, H	384	Bacillus anthracis str. Ames	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L8P2U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C91 Query on C91 Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E] mmCIF format, chain AA [auth F]	AA [auth F] CA [auth G] FA [auth H] J [auth A] M [auth B] AA [auth F], CA [auth G], FA [auth H], J [auth A], M [auth B], Q [auth C], U [auth D], X [auth E]	N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide C₂₄ H₁₈ N₄ O XYCMWFINXXFAFG-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] SDF format, chain L [auth B] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain L [auth B] mmCIF format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain L [auth B]	BA [auth G] EA [auth H] I [auth A] L [auth B] P [auth C] BA [auth G], EA [auth H], I [auth A], L [auth B], P [auth C], T [auth D], W [auth E], Z [auth F]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain GA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain DA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain DA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	DA [auth G] GA [auth H] K [auth A] N [auth B] O [auth B] DA [auth G], GA [auth H], K [auth A], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], Y [auth E]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain DA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain DA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
C91	BindingDB: 4MY9	Ki: min: 44, max: 820 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.216
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/m34my9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.93	α = 98.7
b = 89.883	β = 90.32
c = 104.621	γ = 96.46

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: 2014-06-11

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-06-11
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