9SQ9 | pdb_00009sq9

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

PDB DOI: https://doi.org/10.2210/pdb9SQ9/pdb

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

Deposited: 2025-09-19 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: 2.05 Å
R-Value Free:
0.218 (Depositor), 0.218 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 158.9 kDa
Atom Count: 10,898
Modeled Residue Count: 1,302
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, C [auth B]	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 C], D	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
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain J [auth B] SDF format, chain H [auth C] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain J [auth B] MOL2 format, chain H [auth C] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain J [auth B] mmCIF format, chain H [auth C] mmCIF format, chain F [auth A]	F [auth A], H [auth C], J [auth B], O [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth B] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth B] Focus chain O [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], L [auth B], M [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain N [auth B] MOL2 format, chain P [auth D] MOL2 format, chain N [auth B] mmCIF format, chain P [auth D] mmCIF format, chain N [auth B]	N [auth B], P [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain P [auth D] Interactions & Density Focus chain N [auth B] Focus chain P [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]