8H1R | pdb_00008h1r

Crystal structure of LptDE-YifL complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 
    0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly protein LptD
A, D
924Pseudomonas aeruginosa PAO1Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I5U2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly lipoprotein LptE
B, E
207Pseudomonas aeruginosa PAO1Mutation(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
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UniProt GroupQ9HX32
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized lipoprotein YifL
C, F
67Escherichia coli K-12Mutation(s): 0 
Gene Names: yifL, b4558, JW3781
UniProt
Find proteins for P0ADN6 (Escherichia coli (strain K12))
Explore P0ADN6 
Go to UniProtKB:  P0ADN6
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UniProt GroupP0ADN6
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCJ (Subject of Investigation/LOI)
Query on PCJ
Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.848α = 90
b = 140.475β = 104.39
c = 133.18γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0500404
Chinese Academy of SciencesChinaXDB37020201
National Natural Science Foundation of China (NSFC)China31625009

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-05-21
    Changes: Database references