4MYX | pdb_00004myx

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 (Depositor), 0.260 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

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. 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 LOADING

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] mmCIF format, chain CB [auth H] mmCIF format, chain GA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain U [auth C] mmCIF 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 O [auth B] SDF format, chain OA [auth F] SDF format, chain T [auth C] SDF format, chain VA [auth G] 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 O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain T [auth C] MOL2 format, chain VA [auth G] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth H] mmCIF format, chain FA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain T [auth C] mmCIF format, chain VA [auth G]	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] mmCIF format, chain MA [auth E] mmCIF 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] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth G] mmCIF 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] mmCIF format, chain KA [auth E] mmCIF 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 X [auth C] SDF format, chain Z [auth D] 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 X [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain SA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D]	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 DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain IA [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 R [auth B] SDF format, chain S [auth C] 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 DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain IA [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 R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain UA [auth F] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] mmCIF format, chain AB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain UA [auth F] mmCIF format, chain YA [auth H] mmCIF 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 (Depositor), 0.260 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34myx

Space Group: P 1

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