9UB9 | pdb_00009ub9

Wild-type Bacillus megaterium Penicillin G Acylase

PDB DOI: https://doi.org/10.2210/pdb9UB9/pdb

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

Deposited: 2025-04-02 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: 1.92 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 87.27 kDa
Atom Count: 6,379
Modeled Residue Count: 716
Deposited Residue Count: 747
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60136
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60136
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth B]	C [auth A], H [auth B], J [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth B]	F [auth A], I [auth B], K [auth B], L [auth B], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	D [auth A], E [auth A], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B] mmCIF format, chain G [auth A] mmCIF format, chain T [auth B]	G [auth A], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain T [auth B]