9KPY

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.20 A resolution.

PDB DOI: https://doi.org/10.2210/pdb9KPY/pdb
Entry: 9KPY supersedes: 8I8J

Classification: TRANSFERASE
Organism(s): Enterobacter sp. 638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-24 Released: 2024-12-11
Deposition Author(s): Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267
R-Value Work: 0.207

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.20 A resolution.

Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 117.24 kDa
Atom Count: 8,407
Modelled Residue Count: 989
Deposited Residue Count: 1,045
Unique protein chains: 2

Macromolecules

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(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	173	Enterobacter sp. 638	Mutation(s): 0 Gene Names: coaD, Ent638_0105 EC: 2.7.7.3
UniProt
Find proteins for A4W515 (Enterobacter sp. (strain 638)) Explore A4W515 Go to UniProtKB: A4W515
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4W515
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heptapeptide	G [auth H]	7	Enterobacter sp. 638	Mutation(s): 0 Gene Names: coaD, Ent638_0105
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAE (Subject of Investigation/LOI) Query on PAE Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain H [auth A]	H [auth A] J [auth B] K [auth B] L [auth C] M [auth D] H [auth A], J [auth B], K [auth B], L [auth C], M [auth D], N [auth D], O [auth D], P [auth E], Q [auth F], R [auth F]	PHOSPHONOACETIC ACID C₂ H₅ O₅ P XUYJLQHKOGNDPB-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]