7W3S

The complex structure of Larg1-ADPr from Legionella pneumophila

PDB DOI: https://doi.org/10.2210/pdb7W3S/pdb

Classification: HYDROLASE
Organism(s): Legionella pneumophila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-26 Released: 2022-04-06
Deposition Author(s): Ouyang, S., Guan, H., Li, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.227
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Legionella pneumophila temporally regulates the activity of ADP/ATP translocases by reversible ADP-ribosylation.

Fu, J., Li, P., Guan, H., Huang, D., Song, L., Ouyang, S., Luo, Z.Q.

(2022) mLife

DOI: https://doi.org/10.1002/mlf2.12014

Macromolecule Content

Total Structure Weight: 190.39 kDa
Atom Count: 14,039
Modelled Residue Count: 1,648
Deposited Residue Count: 1,652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion protein Dot	A, B, C, D	413	Legionella pneumophila	Mutation(s): 0 Gene Names: C3927_15620
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 (Subject of Investigation/LOI) Query on AR6 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.227
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.25	α = 90
b = 92.812	β = 105.33
c = 116.053	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
HKL-3000	phasing
SHELXS	phasing
HKL-3000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-04-06
Type: Initial release
Version 1.1: 2022-05-18
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.