5UPU | pdb_00005upu

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the presence of TBK6

PDB DOI: https://doi.org/10.2210/pdb5UPU/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-04 Released: 2017-02-22
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Maltseva, N., Mulligan, R., Gu, M., Sacchettini, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.235 (Depositor), 0.247 (DCC)
R-Value Work:
0.174 (Depositor), 0.182 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the presence of TBK6

Kim, Y., Makowska-Grzyska, M., Maltseva, N., Mulligan, R., Gu, M., Sacchettini, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 42.28 kDa
Atom Count: 2,383
Modeled Residue Count: 332
Deposited Residue Count: 407
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A	407	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: guaB, guaB2, Rv3411c, MTCY78.17 EC: 1.1.1.205
UniProt
Find proteins for P9WKI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKI7 Go to UniProtKB: P9WKI7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WKI7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMP Query on IMP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
6Q9 Query on 6Q9 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	~{N}-(2~{H}-indazol-6-yl)-3,5-dimethyl-1~{H}-pyrazole-4-sulfonamide C₁₂ H₁₃ N₅ O₂ S ZPEANOFCXGJMGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.235 (Depositor), 0.247 (DCC)
R-Value Work: 0.174 (Depositor), 0.182 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.614	α = 90
b = 88.614	β = 90
c = 85.056	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description