5TS2

Crystal structure of a phosphopantetheine adenylyltransferase (CoaD, PPAT) from Pseudomonas aeruginosa bound to dephospho coenzyme A

PDB DOI: https://doi.org/10.2210/pdb5TS2/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa LESB58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-10-27 Released: 2016-11-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244
R-Value Work: 0.180
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a phosphopantetheine adenylyltransferase (CoaD, PPAT) from Pseudomonas aeruginosa bound to dephospho coenzyme A

Edwards, T.E., Davies, D.R., Fairman, J.W., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 117.56 kDa
Atom Count: 7,991
Modelled Residue Count: 971
Deposited Residue Count: 1,002
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A, B, C, D, E A, B, C, D, E, F	167	Pseudomonas aeruginosa LESB58	Mutation(s): 0 Gene Names: coaD, PLES_03601 EC: 2.7.7.3
UniProt
Find proteins for Q9I6D1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I6D1 Go to UniProtKB: Q9I6D1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I6D1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COD Query on COD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	G [auth A] J [auth B] M [auth C] Q [auth D] T [auth E] G [auth A], J [auth B], M [auth C], Q [auth D], T [auth E], W [auth F]	DEPHOSPHO COENZYME A C₂₁ H₃₅ N₇ O₁₃ P₂ S KDTSHFARGAKYJN-IBOSZNHHSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain U [auth E] MOL2 format, chain H [auth A] MOL2 format, chain U [auth E] mmCIF format, chain H [auth A] mmCIF format, chain U [auth E]	H [auth A], U [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth E] Interactions & Density Focus chain H [auth A] Focus chain U [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F]	I [auth A] K [auth B] L [auth B] N [auth C] O [auth C] I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D], V [auth E], X [auth F], Y [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244
R-Value Work: 0.180
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.38	α = 90
b = 101.35	β = 90
c = 105.71	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description