7POW

Crystal structure of phosphatidyl serine synthase (PSS) in transition state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases

Centola, M.Betz, H.Yildiz, O.

(2021) Nat Commun 12: 6982


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CDP-diacylglycerol--serine O-phosphatidyltransferase
A, B
204Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: pssAMJ1212
EC: 2.7.8.8
Membrane Entity: Yes 
UniProt
Find proteins for Q58609 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58609 
Go to UniProtKB:  Q58609
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58609
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SMW (Subject of Investigation/LOI)
Query on SMW

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C [auth A](2S)-2-amino-3-[[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxy-[(2R)-2,3-bis[[(Z)-octadec-9-enoyl]oxy]propoxy]-dihydroxy-lambda^5-phosphanyl]oxy-propanoic acid
C51 H92 N4 O18 P2
SMGJVPWANUHLFX-OTXLWCCGSA-N
58A (Subject of Investigation/LOI)
Query on 58A

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P [auth B]5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
C48 H85 N3 O15 P2
WVVFFOKRFKIBHD-ZIPNUMAKSA-N
OLC
Query on OLC

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J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
SER
Query on SER

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U [auth B]SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
CA
Query on CA

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D [auth A],
Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
S [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
S [auth B],
T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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E [auth A],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.35α = 90
b = 61.22β = 118.723
c = 79.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Advisory