4MY8

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor Q21

PDB DOI: https://doi.org/10.2210/pdb4MY8/pdb

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

Deposited: 2013-09-27 Released: 2013-11-13
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Gorla, S.K., Kavitha, M., Cuny, G., Hedstrom, L., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.225
R-Value Work: 0.173
R-Value Observed: 0.176

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 Q21

Kim, Y., Makowska-Grzyska, M., Gu, M., Gorla, S.K., Kavitha, M., Cuny, G., Hedstrom, L., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 166.73 kDa
Atom Count: 10,378
Modelled Residue Count: 1,334
Deposited Residue Count: 1,536
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	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q21 Query on Q21 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain R [auth B] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth D]	F [auth A], M [auth B], R [auth B], Y [auth D]	(2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide C₂₅ H₁₉ N₃ O₃ QCNXGTHMVPSAAC-INIZCTEOSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain R [auth B] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain R [auth B] Focus chain Y [auth D]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D]	E [auth A], L [auth B], S [auth C], X [auth D]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain W [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D]	AA [auth D] G [auth A] H [auth A] N [auth B] P [auth B] AA [auth D], G [auth A], H [auth A], N [auth B], P [auth B], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain W [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth C] MOL2 format, chain K [auth A] MOL2 format, chain U [auth C]	K [auth A], U [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth C] Interactions & Density Focus chain K [auth A] Focus chain U [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D]	BA [auth D] I [auth A] J [auth A] O [auth B] Q [auth B] BA [auth D], I [auth A], J [auth A], O [auth B], Q [auth B], T [auth C], V [auth C], Z [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
Q21	BindingDB: 4MY8	Ki: min: 17, max: 24 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.225
R-Value Work: 0.173
R-Value Observed: 0.176
Space Group: P 1 2 1
Diffraction Data: https://doi.org/10.18430/M34MY8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.433	α = 90
b = 56.226	β = 89.83
c = 111.395	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: 2013-11-13

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-11-13
Type: Initial release
Version 1.1: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description