9Y43 | pdb_00009y43

3-hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.

PDB DOI: https://doi.org/10.2210/pdb9Y43/pdb

Classification: LIGASE
Organism(s): Nitrosopumilus maritimus SCM1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-02 Released: 2025-10-01
Deposition Author(s): Johnson, J.A., Yilmaz, M., Tosun, B., Wakatsuki, S., Demirci, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.250 (Depositor), 0.255 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of 3-Hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus

Johnson, J.A., Tosun, B., Yilmaz, M., Tolar, B., Yoshikuni, Y., Francis, C., Doukov, T., Yokoi, S., Wakatsuki, S., Demirci, H.

To be published.

Macromolecule Content

Total Structure Weight: 153.37 kDa
Atom Count: 10,797
Modeled Residue Count: 1,394
Deposited Residue Count: 1,410
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxypropionate--CoA ligase [ADP-forming]	A, B	705	Nitrosopumilus maritimus SCM1	Mutation(s): 0 Gene Names: Nmar_1309 EC: 6.2.1
UniProt
Find proteins for A9A2G6 (Nitrosopumilus maritimus (strain SCM1)) Explore A9A2G6 Go to UniProtKB: A9A2G6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9A2G6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP 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]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
3OH Query on 3OH Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	3-HYDROXY-PROPANOIC ACID C₃ H₆ O₃ ALRHLSYJTWAHJZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]