3COZ

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.0 Ang resolution- in complex with sulphonamide inhibitor 4

PDB DOI: https://doi.org/10.2210/pdb3COZ/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-03-29 Released: 2008-10-07
Deposition Author(s): Ciulli, A., Chirgadze, D.Y., Blundell, T.L., Abell, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate.

Ciulli, A., Scott, D.E., Ando, M., Reyes, F., Saldanha, S.A., Tuck, K.L., Chirgadze, D.Y., Blundell, T.L., Abell, C.

(2008) Chembiochem 9: 2606-2611

PubMed: 18821554 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cbic.200800437
Primary Citation of Related Structures:
3COV, 3COW, 3COY, 3COZ

Organizational Affiliation

University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK. ac313@cam.ac.uk

Macromolecule Content

Total Structure Weight: 64.5 kDa
Atom Count: 4,634
Modelled Residue Count: 566
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate synthetase	A, B	301	Mycobacterium tuberculosis	Mutation(s): 2 Gene Names: panC EC: 6.3.2.1
UniProt
Find proteins for P9WIL5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIL5 Go to UniProtKB: P9WIL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
54H Query on 54H Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B]	D [auth A], K [auth B]	5'-O-(D-valylsulfamoyl)adenosine C₁₅ H₂₃ N₇ O₇ S TXCZGHBHNXNXMA-FGOODDOWSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
54H	Binding MOAD: 3COZ	Kd: 2700 (nM) from 1 assay(s)
54H	PDBBind: 3COZ	Kd: 2700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.6	α = 90
b = 71.23	β = 99.56
c = 82.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description

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3COZ

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.0 Ang resolution- in complex with sulphonamide inhibitor 4

Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)