9YMM | pdb_00009ymm

Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine

PDB DOI: https://doi.org/10.2210/pdb9YMM/pdb

Classification: LIGASE
Organism(s): Moraxella catarrhalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-10 Released: 2025-10-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free:
0.253 (Depositor), 0.252 (DCC)
R-Value Work:
0.214 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (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

Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine

Enayati, P., Liu, L., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 241.98 kDa
Atom Count: 15,316
Modeled Residue Count: 1,897
Deposited Residue Count: 2,076
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate--tRNA ligase	A, B, C, D	519	Moraxella catarrhalis	Mutation(s): 0 Gene Names: gltX, AO370_0559 EC: 6.1.1.17
UniProt
Find proteins for A0AB36DQE3 (Moraxella catarrhalis) Explore A0AB36DQE3 Go to UniProtKB: A0AB36DQE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AB36DQE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 BA [auth C] SDF format, chain E [auth A] SDF format, chain IA [auth D] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain U [auth B]	BA [auth C], E [auth A], IA [auth D], U [auth B]	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE C₁₅ H₂₁ N₇ O₉ S YBRKRYFZKHICLS-WERHYGNASA-N		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain IA [auth D] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain IA [auth D] Focus chain U [auth B]
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain JA [auth D] MOL2 format, chain JA [auth D] mmCIF format, chain JA [auth D]	JA [auth D]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Interactions & Density Focus chain JA [auth D]
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain WA [auth D] SDF format, chain W [auth B] SDF format, chain VA [auth D] SDF format, chain UA [auth D] SDF format, chain TA [auth D] SDF format, chain T [auth A] SDF format, chain SA [auth D] SDF format, chain S [auth A] SDF format, chain RA [auth D] SDF format, chain R [auth A] SDF format, chain QA [auth D] SDF format, chain Q [auth A] SDF format, chain PA [auth D] SDF format, chain P [auth A] SDF format, chain OA [auth D] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain FA [auth C] SDF format, chain F [auth A] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] CA [auth C] DA [auth C] EA [auth C] F [auth A] AA [auth B], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], SA [auth D], T [auth A], TA [auth D], UA [auth D], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free: 0.253 (Depositor), 0.252 (DCC)
R-Value Work: 0.214 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.713	α = 90
b = 124.225	β = 90
c = 458.212	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394