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
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 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

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 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 AA [auth F] 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] MOL2 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] mmCIF 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]	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 L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	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]

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

View Full Validation Report

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