4MYX

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Bacillus anthracis str. Ame complexed with P32

PDB DOI: https://doi.org/10.2210/pdb4MYX/pdb

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

Deposited: 2013-09-28 Released: 2014-07-23
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: 2.70 Å
R-Value Free: 0.260
R-Value Work: 0.218
R-Value Observed: 0.220

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 a Internal Deletion of CBS Domain from Bacillus anthracis str. Ame complexed with P32

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

To be published.

Macromolecule Content

Total Structure Weight: 333.56 kDa
Atom Count: 21,740
Modelled Residue Count: 2,814
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2F0 Query on 2F0 Download Ideal Coordinates CCD File SDF format, chain CB [auth H] SDF format, chain GA [auth E] SDF format, chain J [auth A] SDF format, chain NA [auth E] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain GA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D]	CB [auth H] GA [auth E] J [auth A] NA [auth E] P [auth B] CB [auth H], GA [auth E], J [auth A], NA [auth E], P [auth B], PA [auth F], U [auth C], Y [auth D]	2-chloro-5-{[(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)carbamoyl]amino}benzamide C₁₉ H₂₁ Cl N₄ O₃ NRJRCKIOCQMNMC-BHGWPJFGSA-N		Interactions Focus chain CB [auth H] Focus chain GA [auth E] Focus chain J [auth A] Focus chain NA [auth E] Focus chain P [auth B] Focus chain PA [auth F] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CB [auth H] Focus chain GA [auth E] Focus chain J [auth A] Focus chain NA [auth E] Focus chain P [auth B] Focus chain PA [auth F] Focus chain U [auth C] Focus chain Y [auth D]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain BB [auth H] SDF format, chain FA [auth E] SDF format, chain I [auth A] SDF format, chain OA [auth F] SDF format, chain T [auth C] SDF format, chain VA [auth G] SDF format, chain O [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth H] MOL2 format, chain FA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain T [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain O [auth B]	BA [auth D] BB [auth H] FA [auth E] I [auth A] O [auth B] BA [auth D], BB [auth H], FA [auth E], I [auth A], O [auth B], OA [auth F], T [auth C], VA [auth G]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain BA [auth D] Focus chain BB [auth H] Focus chain FA [auth E] Focus chain I [auth A] Focus chain O [auth B] Focus chain OA [auth F] Focus chain T [auth C] Focus chain VA [auth G] Interactions & Density Focus chain BA [auth D] Focus chain BB [auth H] Focus chain FA [auth E] Focus chain I [auth A] Focus chain O [auth B] Focus chain OA [auth F] Focus chain T [auth C] Focus chain VA [auth G]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain MA [auth E] SDF format, chain N [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A]	MA [auth E], N [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain MA [auth E] Focus chain N [auth A] Interactions & Density Focus chain MA [auth E] Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain WA [auth G] SDF format, chain XA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G]	W [auth C], WA [auth G], XA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Interactions & Density Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain KA [auth E] SDF format, chain M [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain M [auth A]	KA [auth E], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain KA [auth E] Focus chain M [auth A] Interactions & Density Focus chain KA [auth E] Focus chain M [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth D] SDF format, chain JA [auth E] SDF format, chain Q [auth B] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain TA [auth F] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth C]	AA [auth D] CA [auth D] JA [auth E] Q [auth B] RA [auth F] AA [auth D], CA [auth D], JA [auth E], Q [auth B], RA [auth F], SA [auth F], TA [auth F], V [auth C], X [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain JA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain V [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain JA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain V [auth C] Focus chain X [auth C] Focus chain Z [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain DB [auth H] SDF format, chain IA [auth E] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain QA [auth F] SDF format, chain UA [auth F] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] MOL2 format, chain AB [auth H] MOL2 format, chain DB [auth H] MOL2 format, chain IA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain QA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H]	AB [auth H] DA [auth D] DB [auth H] EA [auth D] HA [auth E] AB [auth H], DA [auth D], DB [auth H], EA [auth D], HA [auth E], IA [auth E], K [auth A], L [auth A], LA [auth E], QA [auth F], R [auth B], S [auth C], UA [auth F], YA [auth H], ZA [auth H]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth C] Focus chain UA [auth F] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain AB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth C] Focus chain UA [auth F] Focus chain YA [auth H] Focus chain ZA [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
2F0	BindingDB: 4MYX	Ki: min: 1.5, max: 8 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.260
R-Value Work: 0.218
R-Value Observed: 0.220
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M34MYX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.365	α = 81.41
b = 89.82	β = 90.42
c = 104.502	γ = 83.5

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: 2014-07-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-07-23
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