9L8V | pdb_00009l8v

PyrN C-terminl domain in complex with L-glutamyl-sulfamoyl-adenosine (GSA)

PDB DOI: https://doi.org/10.2210/pdb9L8V/pdb

Classification: LIGASE
Organism(s): Streptomyces candidus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-12-28 Released: 2025-12-31
Deposition Author(s): Du, Y.L., Zhao, G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.187 (Depositor), 0.189 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: in silico
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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

PyrN C-terminl domain in complex with L-glutamyl-sulfamoyl-adenosine (GSA)

Du, Y.L., Du, Y.L.

To be published.

Macromolecule Content

Total Structure Weight: 242.61 kDa
Atom Count: 17,498
Modeled Residue Count: 2,129
Deposited Residue Count: 2,184
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine-tRNA ligase	A, B, C [auth D], D [auth B00Z]	546	Streptomyces candidus	Mutation(s): 0 Gene Names: pyrN, prfJ
UniProt
Find proteins for A0A516ELE7 (Streptomyces candidus) Explore A0A516ELE7 Go to UniProtKB: A0A516ELE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A516ELE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSU (Subject of Investigation/LOI) Query on GSU Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain S [auth D] SDF format, chain X [auth B00Z] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] MOL2 format, chain X [auth B00Z] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D] mmCIF format, chain X [auth B00Z] mmCIF format, chain H [auth A]	H [auth A], N [auth B], S [auth D], X [auth B00Z]	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE C₁₅ H₂₁ N₇ O₉ S YBRKRYFZKHICLS-WERHYGNASA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth D] Focus chain X [auth B00Z] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth D] Focus chain X [auth B00Z]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain T [auth B00Z] SDF format, chain U [auth B00Z] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain T [auth B00Z] MOL2 format, chain U [auth B00Z] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain T [auth B00Z] mmCIF format, chain U [auth B00Z] mmCIF format, chain K [auth B]	E [auth A] I [auth B] J [auth B] K [auth B] O [auth D] E [auth A], I [auth B], J [auth B], K [auth B], O [auth D], P [auth D], T [auth B00Z], U [auth B00Z]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain T [auth B00Z] Focus chain U [auth B00Z] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain T [auth B00Z] Focus chain U [auth B00Z]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain W [auth B00Z] SDF format, chain V [auth B00Z] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain W [auth B00Z] MOL2 format, chain V [auth B00Z] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain W [auth B00Z] mmCIF format, chain V [auth B00Z] mmCIF format, chain M [auth B]	F [auth A] G [auth A] L [auth B] M [auth B] Q [auth D] F [auth A], G [auth A], L [auth B], M [auth B], Q [auth D], R [auth D], V [auth B00Z], W [auth B00Z]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain V [auth B00Z] Focus chain W [auth B00Z] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain V [auth B00Z] Focus chain W [auth B00Z]