4MY8 | pdb_00004my8

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 (Depositor), 0.230 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

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
Modeled 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] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth B] mmCIF 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] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF 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] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF 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] mmCIF format, chain K [auth A] mmCIF 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] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF 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 (Depositor), 0.230 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34my8

Space Group: P 1 2 1

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

View Full Validation Report

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