8H1R | pdb_00008h1r

Crystal structure of LptDE-YifL complex

PDB DOI: https://doi.org/10.2210/pdb8H1R/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1, Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-03 Released: 2023-10-25
Deposition Author(s): Luo, Q., Huang, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.264 (Depositor), 0.265 (DCC)
R-Value Work:
0.234 (Depositor), 0.237 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Surface lipoprotein sorting by crosstalk between Lpt and Lol pathways in gram-negative bacteria

Luo, Q., Wang, C., Qiao, S., Yu, S., Chen, L., Kim, S., Wang, K., Zheng, J., Zhang, Y., Wu, F., Lei, X., Lou, J., Hennig, M., Im, W., Miao, L., Zhou, M., Bei, W., Huang, Y.

(2025) Nat Commun 16: 4357

DOI: https://doi.org/10.1038/s41467-025-59660-y

Macromolecule Content

Total Structure Weight: 270.75 kDa
Atom Count: 15,349
Modeled Residue Count: 1,893
Deposited Residue Count: 2,396
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly protein LptD	A, D	924	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lptD, imp, ostA, PA0595
UniProt
Find proteins for Q9I5U2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5U2 Go to UniProtKB: Q9I5U2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I5U2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	B, E	207	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lptE, PA3988
UniProt
Find proteins for Q9HX32 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HX32 Go to UniProtKB: Q9HX32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HX32
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein YifL	C, F	67	Escherichia coli K-12	Mutation(s): 0 Gene Names: yifL, b4558, JW3781
UniProt
Find proteins for P0ADN6 (Escherichia coli (strain K12)) Explore P0ADN6 Go to UniProtKB: P0ADN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ADN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCJ (Subject of Investigation/LOI) Query on PCJ Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth A]	G [auth A], H [auth D]	(2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE C₅₄ H₁₀₅ N O₆ S GBQDHEZHWNJSLG-OKPYTHRESA-N		Interactions Focus chain G [auth A] Focus chain H [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.264 (Depositor), 0.265 (DCC)
R-Value Work: 0.234 (Depositor), 0.237 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.848	α = 90
b = 140.475	β = 104.39
c = 133.18	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Luo, Q.

Huang, Y.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0500404
Chinese Academy of Sciences	China	XDB37020201
National Natural Science Foundation of China (NSFC)	China	31625009