9V14 | pdb_00009v14

crystal structure of the enzyme-product complex of L-azetidine-2-carboxylate hydrolase

PDB DOI: https://doi.org/10.2210/pdb9V14/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas sp. A2C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-19 Released: 2025-06-04
Deposition Author(s): Toyoda, M., Mizutani, K., Mikami, B., Wackett, L.P., Esaki, N., Kurihara, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.93 Å
R-Value Free:
0.140 (Depositor), 0.131 (DCC)
R-Value Work:
0.116 (Depositor), 0.109 (DCC)

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

Research for the crystal structure of L-azetidine-2-carboxylate hydrolase

Toyoda, M., Mizutani, K., Mikami, B., Wackett, L.P., Esaki, N., Kurihara, T.

To be published.

Macromolecule Content

Total Structure Weight: 27.68 kDa
Atom Count: 2,793
Modeled Residue Count: 240
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-azetidine-2-carboxylate hydrolase	A	240	Pseudomonas sp. A2C	Mutation(s): 0 EC: 3.8.1.2 (PDB Primary Data), 3.5 (UniProt)
UniProt
Find proteins for B2Z3V8 (Pseudomonas sp. (strain A2C)) Explore B2Z3V8 Go to UniProtKB: B2Z3V8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2Z3V8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
42B (Subject of Investigation/LOI) Query on 42B Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-AMINO-2-HYDROXYBUTANOIC ACID C₄ H₉ N O₃ IVUOMFWNDGNLBJ-GSVOUGTGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]