4MY1

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Bacillus anthracis str. Ames complexed with P68

PDB DOI: https://doi.org/10.2210/pdb4MY1/pdb

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

Deposited: 2013-09-26 Released: 2014-01-01
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: 2.60 Å
R-Value Free: 0.253
R-Value Work: 0.194
R-Value Observed: 0.197

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 a Internal Deletion of CBS Domain from Bacillus anthracis str. Ames complexed with P68

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

To be published.

Macromolecule Content

Total Structure Weight: 331.58 kDa
Atom Count: 21,010
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 str. Ames	Mutation(s): 0 Gene Names: BAS0011, BA_0008, GBAA_0008, guaB 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P68 Query on P68 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], S [auth E], V [auth G], X [auth H]	1-(4-bromophenyl)-3-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea C₁₈ H₂₀ Br N₃ O₂ DSTKQECXQMKQLN-WSDLNYQXSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth G] Focus chain X [auth H]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain Q [auth E] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain O [auth D] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], T [auth F], U [auth G], W [auth H]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.253
R-Value Work: 0.194
R-Value Observed: 0.197
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/m34my1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.22	α = 81.13
b = 89.391	β = 89.95
c = 103.987	γ = 83.59

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: 2014-01-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-01-01
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