9SQJ | pdb_00009sqj

Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes with bound AMPPNP

PDB DOI: https://doi.org/10.2210/pdb9SQJ/pdb

Classification: LIGASE
Organism(s): Streptococcus pyogenes MGAS10270
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-22 Released: 2025-10-08
Deposition Author(s): Voelpel, S.V., Stehle, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.217 (Depositor), 0.236 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (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

Crystal Structure of the MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pyogenes

Voelpel, S.V., Stehle, T.

To be published.

Macromolecule Content

Total Structure Weight: 158.67 kDa
Atom Count: 11,032
Modeled Residue Count: 1,308
Deposited Residue Count: 1,402
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT	A [auth AAA], C [auth BBB]	438	Streptococcus pyogenes MGAS10270	Mutation(s): 0 Gene Names: murT, SAMEA1711581_01631 EC: 6.3.5.13
UniProt
Find proteins for A0A8B6J667 (Streptococcus pyogenes) Explore A0A8B6J667 Go to UniProtKB: A0A8B6J667
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8B6J667
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD	B [auth CCC], D [auth DDD]	263	Streptococcus pyogenes MGAS10270	Mutation(s): 0 Gene Names: gatD, E0F67_01185 EC: 6.3.5.13 (PDB Primary Data), 3.5.1.2 (PDB Primary Data)
UniProt
Find proteins for A0A5S4TG60 (Streptococcus pyogenes) Explore A0A5S4TG60 Go to UniProtKB: A0A5S4TG60
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5S4TG60
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain K [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain K [auth BBB] mmCIF format, chain G [auth AAA] mmCIF format, chain K [auth BBB]	G [auth AAA], K [auth BBB]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain G [auth AAA] Focus chain K [auth BBB] Interactions & Density Focus chain G [auth AAA] Focus chain K [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain L [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain L [auth BBB] mmCIF format, chain H [auth AAA] mmCIF format, chain L [auth BBB]	H [auth AAA], L [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain L [auth BBB] Interactions & Density Focus chain H [auth AAA] Focus chain L [auth BBB]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain I [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain I [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain I [auth BBB]	E [auth AAA], I [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain I [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain I [auth BBB]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain J [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain J [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain J [auth BBB]	F [auth AAA], J [auth BBB]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain J [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain J [auth BBB]