3OAA

Structure of the E.coli F1-ATP synthase inhibited by subunit Epsilon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for inhibition of bacterial ATP synthase by subunit epsilon of the rotor stalk

Cingolani, G.Duncan, T.M.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A,
AA [auth a],
B,
C,
I,
J,
K,
Q,
R,
S,
Y,
Z
513Escherichia coli DH1Mutation(s): 0 
Gene Names: atpAEcDH1_4233
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for P0ABB0 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABB0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta459Escherichia coli DH1Mutation(s): 1 
Gene Names: atpDEcDH1_4235
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for P0ABB4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABB4
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UniProt GroupP0ABB4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chainEA [auth e],
G,
O,
W
286Escherichia coli DH1Mutation(s): 0 
Gene Names: EcDH1_4234
Membrane Entity: Yes 
UniProt
Find proteins for P0ABA6 (Escherichia coli (strain K12))
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UniProt GroupP0ABA6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainFA [auth f],
H,
P,
X
138Escherichia coli DH1Mutation(s): 0 
Gene Names: atpCEcDH1_4236
Membrane Entity: Yes 
UniProt
Find proteins for P0A6E6 (Escherichia coli (strain K12))
Explore P0A6E6 
Go to UniProtKB:  P0A6E6
Entity Groups  
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UniProt GroupP0A6E6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

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GA [auth A]
GB [auth Q]
IA [auth B]
IB [auth R]
KA [auth C]
GA [auth A],
GB [auth Q],
IA [auth B],
IB [auth R],
KA [auth C],
KB [auth S],
SB [auth Y],
TA [auth I],
UB [auth Z],
VA [auth J],
WB [auth a],
XA [auth K]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ADP
Query on ADP

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MA [auth D],
MB [auth T],
YB [auth b],
ZA [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4
Query on SO4

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AC [auth b]
BB [auth L]
BC [auth c]
CB [auth M]
CC [auth d]
AC [auth b],
BB [auth L],
BC [auth c],
CB [auth M],
CC [auth d],
DB [auth N],
EB [auth O],
FB [auth P],
OA [auth D],
OB [auth T],
PA [auth E],
PB [auth U],
QA [auth F],
QB [auth V],
RA [auth G],
RB [auth W],
SA [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

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AB [auth L]
HA [auth A]
HB [auth Q]
JA [auth B]
JB [auth R]
AB [auth L],
HA [auth A],
HB [auth Q],
JA [auth B],
JB [auth R],
LA [auth C],
LB [auth S],
NA [auth D],
NB [auth T],
TB [auth Y],
UA [auth I],
VB [auth Z],
WA [auth J],
XB [auth a],
YA [auth K],
ZB [auth b]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 435.97α = 90
b = 183β = 108.99
c = 225.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description