9UEW | pdb_00009uew

Wild-type Bacillus megaterium Penicillin G Acylase with Non-Covalently Bound Phenylacetic Acid

PDB DOI: https://doi.org/10.2210/pdb9UEW/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Priestia megaterium
Expression System: Priestia megaterium
Mutation(s): No

Deposited: 2025-04-09 Released: 2026-02-18
Deposition Author(s): Kaewsasan, C., Rojviriya, C., Yuvaniyama, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.188 (Depositor), 0.188 (DCC)
R-Value Work:
0.142 (Depositor), 0.142 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Capturing Catalysis: Structural Insights into the Acyl-Enzyme Intermediate of Priestia megaterium Penicillin G Acylase

Kaewsasan, C., Rojviriya, C., Oonanant, W., Prathumrat, N., Koinueng, W., Yuvaniyama, J.

(2026) ACS Catal

DOI: https://doi.org/10.1021/acscatal.6c00015

Macromolecule Content

Total Structure Weight: 88.03 kDa
Atom Count: 6,540
Modeled Residue Count: 725
Deposited Residue Count: 747
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase	A	210	Priestia megaterium	Mutation(s): 0 Gene Names: pac, pga EC: 3.5.1.11
UniProt
Find proteins for Q60136 (Priestia megaterium) Explore Q60136 Go to UniProtKB: Q60136
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60136
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase subunit beta	B	537	Priestia megaterium	Mutation(s): 0 Gene Names: pac, pga EC: 3.5.1.11
UniProt
Find proteins for Q60136 (Priestia megaterium) Explore Q60136 Go to UniProtKB: Q60136
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60136
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAC (Subject of Investigation/LOI) Query on PAC Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain CA [auth B]	CA [auth B]	2-PHENYLACETIC ACID C₈ H₈ O₂ WLJVXDMOQOGPHL-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain M [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain M [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain M [auth B]	M [auth B], R [auth B], S [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain M [auth B] Focus chain R [auth B] Focus chain S [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain P [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	AA [auth B] BA [auth B] C [auth A] D [auth A] E [auth A] AA [auth B], BA [auth B], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], P [auth B], Q [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B]	DA [auth B], EA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain J [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain J [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain J [auth A]	FA [auth B], GA [auth B], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain J [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain J [auth A]