7W15 | pdb_00007w15

Crystal Structure of MPH-E in complex with GTP and Erythromycin

PDB DOI: https://doi.org/10.2210/pdb7W15/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-11-19 Released: 2023-04-26
Deposition Author(s): Qi, Q., Kuang, L., Jiang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.196 (Depositor), 0.200 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Acinetobacter baumannii Macrolide Phosphotransferases E Reveal the Novel Catalysis Mechanism

Qi, Q., Kuang, L., Jiang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 72.08 kDa
Atom Count: 5,733
Modeled Residue Count: 587
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide 2'-phosphotransferase	A [auth B], B [auth A]	302	Acinetobacter baumannii	Mutation(s): 0 Gene Names: mph(E)
UniProt
Find proteins for A5Y459 (Acinetobacter baumannii) Explore A5Y459 Go to UniProtKB: A5Y459
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5Y459
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ERY (Subject of Investigation/LOI) Query on ERY Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain C [auth B] MOL2 format, chain J [auth A] MOL2 format, chain C [auth B] mmCIF format, chain J [auth A] mmCIF format, chain C [auth B]	C [auth B], J [auth A]	ERYTHROMYCIN A C₃₇ H₆₇ N O₁₃ ULGZDMOVFRHVEP-RWJQBGPGSA-N		Interactions Focus chain C [auth B] Focus chain J [auth A] Interactions & Density Focus chain C [auth B] Focus chain J [auth A]
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain D [auth B] MOL2 format, chain K [auth A] MOL2 format, chain D [auth B] mmCIF format, chain K [auth A] mmCIF format, chain D [auth B]	D [auth B], K [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain D [auth B] Focus chain K [auth A] Interactions & Density Focus chain D [auth B] Focus chain K [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] G [auth B] L [auth A] M [auth A] E [auth B], F [auth B], G [auth B], L [auth A], M [auth A], N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]