9DHN | pdb_00009dhn

Crystal structure of PIsnA complexed with an imine intermediate

PDB DOI: https://doi.org/10.2210/pdb9DHN/pdb

Classification: TRANSFERASE
Organism(s): Photorhabdus luminescens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-04 Released: 2025-07-16
Deposition Author(s): Kim, W., Zhang, Y.J., Guo, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.259 (Depositor), 0.259 (DCC)
R-Value Work:
0.238 (Depositor), 0.238 (DCC)
R-Value Observed:
0.240 (Depositor)

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

Studies of Isonitrile Synthases Help Elucidate the Mechanism of Isonitrile Installation

Chen, T.Y., Kim, W., Guo, M., Yao, A., Zhang, Y.J., Chang, W.C.

(2025) ACS Catal : 12005-12013

DOI: https://doi.org/10.1021/acscatal.5c03282

Macromolecule Content

Total Structure Weight: 73.57 kDa
Atom Count: 5,129
Modeled Residue Count: 624
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-tyrosine/L-tryptophan isonitrile synthase family protein	A, B	315	Photorhabdus luminescens	Mutation(s): 0 Gene Names: GPY51_01455
UniProt
Find proteins for A0A1G5Q840 (Photorhabdus luminescens) Explore A0A1G5Q840 Go to UniProtKB: A0A1G5Q840
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1G5Q840
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A46 (Subject of Investigation/LOI) Query on A1A46 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]	(2S)-2-{[(2S,3S)-1,3-dihydroxy-4-oxopentan-2-yl]amino}-3-(4-hydroxyphenyl)propanoic acid C₁₄ H₁₉ N O₆ FFYADCDWUVDZPP-RWMBFGLXSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PG6 (Subject of Investigation/LOI) Query on PG6 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]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PG0 (Subject of Investigation/LOI) Query on PG0 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]