9LEH | pdb_00009leh

nitrile synthetase ArtA

PDB DOI: https://doi.org/10.2210/pdb9LEH/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Penicillium aurantiogriseum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-07 Released: 2026-01-14
Deposition Author(s): Ma, H.L., Zhang, K.K.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.234 (Depositor), 0.232 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Mechanistic Basis for Nitrile Synthetase by an Argininosuccinate Synthetase-Like Enzyme

Zeng, Y., Zhang, K., Lu, T., Yin, X., Wang, Q., Xiong, L., Guo, H., Li, J., Lu, X., Liu, L., Ma, H., Gao, Z.

(2025) ACS Catal 15: 16254-16267

DOI: https://doi.org/10.1021/acscatal.5c04243

Macromolecule Content

Total Structure Weight: 96.93 kDa
Atom Count: 6,552
Modeled Residue Count: 761
Deposited Residue Count: 870
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nitrile synthetase	A, B	435	Penicillium aurantiogriseum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A], D [auth A], F [auth A], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	G [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]