6I8W

Crystal structure of a membrane phospholipase A, a novel bacterial virulence factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural, mechanistic and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa

Bleffert, F.Granzin, J.Caliskan, M.Schott-Verdugo, S.N.Siebers, M.Thiele, B.Rahme, L.G.Felgner, S.Dormann, P.Gohlke, H.Batra-Safferling, R.Erich-Jager, K.Kovacic, F.Radhakrishnan, A.

(2022) Elife 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha/beta fold hydrolaseA, B322Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
lip3AOY09_04297C8257_11100DN070_25360NCTC13719_02038PAMH19_2121lip4IPC112_03780IPC113_08930IPC114_03625IPC115_09405IPC127_05560IPC128_06540IPC129_03345IPC1307_00860IPC130_08665IPC1316_09375IPC1318_08745IPC1319_16950IPC131_04335IPC1322_14870IPC1323_13930IPC1324_14375IPC1325_12645IPC1326_14375IPC1327_16035IPC1328_06960IPC132_01290IPC1330_16820IPC1332_10860IPC1333_03220IPC1335_10625IPC1339_12695IPC133_10895IPC1340_11750IPC1342_09065IPC134_04330IPC135_13240IPC139_12065IPC140_07590IPC141_12275IPC142_09670IPC143_09835IPC1479_15145IPC1480_15400IPC1481_17765IPC1482_05475IPC1485_13785IPC1486_09275IPC1487_00725IPC1492_03545IPC1496_14825IPC1508_10510IPC1509_14510IPC150_14420IPC1510_04185IPC1511_01485IPC1512_04990IPC1513_22230IPC1514_18145IPC151_11735IPC1520_18175IPC1521_13520IPC1523_03565IPC152_09675IPC1583_10040IPC1585_11295IPC1586_07005IPC1588_09985IPC1591_08420IPC1592_11135IPC1593_06870IPC1594_02950IPC1596_09480IPC1597_09455IPC1598_01940IPC1599_02965IPC1600_16830IPC1601_10740IPC1602_17205IPC1604_01785IPC1605_05415IPC1606_04785IPC162_09840IPC163_03785IPC164_08520IPC165_03785IPC166_05485IPC167_03785IPC169_03785IPC170_08520IPC171_16410IPC172_15220IPC173_20435IPC174_05780IPC175_12930IPC176_11685IPC177_13040IPC181_09005IPC184_02600IPC29_17495IPC34_13455IPC35_15405IPC36_13440IPC40_08670IPC41_10535IPC42_19560IPC43_07970IPC44_14615IPC45_08100IPC46_01985IPC47_11160IPC48_15135IPC49_11575IPC58_10875IPC603_06160IPC604_07335IPC605_06335IPC606_06330IPC611_13065IPC612_10415IPC613_14170IPC614_05265IPC615_05975IPC616_11535IPC618_14000IPC620_19270IPC624_15910IPC64_06555IPC65_26050IPC66_10005IPC70_06660IPC71_07570IPC72_11115IPC73_14655IPC74_10445IPC76_12750IPC77_07415IPC78_07425PA52Ts2_4318

EC: 3.1.1.3
UniProt
Find proteins for Q9KJG6 (Pseudomonas aeruginosa)
Explore Q9KJG6 
Go to UniProtKB:  Q9KJG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KJG6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
MYR
Query on MYR

Download Ideal Coordinates CCD File 
C [auth A]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
11A
Query on 11A

Download Ideal Coordinates CCD File 
I [auth B]UNDECANOIC ACID
C11 H22 O2
ZDPHROOEEOARMN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
L [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CO2
Query on CO2

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B]
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, B L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.871α = 90
b = 133.871β = 90
c = 212.358γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2022-05-18
    Changes: Database references, Structure summary