9V5S | pdb_00009v5s

Crystal structure of EF-Tu from Mycoplasma pneumoniae

PDB DOI: https://doi.org/10.2210/pdb9V5S/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Mycoplasmoides pneumoniae M129
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-26 Released: 2025-10-29
Deposition Author(s): Liu, Y.H., Wang, W.M., Wang, H.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.242 (Depositor), 0.243 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural insights of the first elongation factor EF-Tu complexes from mycoplasma

Liu, Y.H., Ma, D., Yao, H., Gong, W., Xie, L., Zhao, Y., Zhao, Y., Wang, W.M., Wang, H.F.

(2026) J Mol Struct 1350

Macromolecule Content

Total Structure Weight: 174.72 kDa
Atom Count: 12,463
Modeled Residue Count: 1,529
Deposited Residue Count: 1,576
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Tu	A, B, C, D	394	Mycoplasmoides pneumoniae M129	Mutation(s): 0 Gene Names: tuf, MPN_665, MP177 EC: 3.6.5.3
UniProt
Find proteins for P23568 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P23568 Go to UniProtKB: P23568
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23568
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]