7A0X

Structure of dimeric sodium proton antiporter NhaA, at pH 6.0, crystallized with chimeric Fab antibodies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular determinants for substrate uptake in electrogenic sodium/proton antiporters

Fippel, A.Mir, S.H.Wirth, C.Gross, N.M.Lentes, C.J.Bialas, E.Frank, F.Ulbrich, M.H.Andrade, S.L.A.Kulik, A.Hunte, C.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)/H(+) antiporter NhaA
A, B
406Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: nhaASTM0039
Membrane Entity: Yes 
UniProt
Find proteins for Q8ZRZ3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZRZ3 
Go to UniProtKB:  Q8ZRZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZRZ3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain
C, E
252Gallus gallusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain
D, F
210Gallus gallusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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G [auth A]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PE
Query on 3PE

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M [auth B]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
3PH
Query on 3PH

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H [auth A],
K [auth B],
L [auth B]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
PG4
Query on PG4

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J [auth A],
O [auth B],
R [auth E],
S [auth E]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4
Query on PO4

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I [auth A],
N [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA

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U [auth F]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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P [auth C],
Q [auth C],
T [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.01α = 90
b = 91.713β = 109.798
c = 139.997γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBIOSS - EXC-294
German Research Foundation (DFG)GermanyCIBSS - EXC-2189 - Project ID 390939984
German Research Foundation (DFG)GermanyCRC - 1381 - Project ID ID 403222702
German Research Foundation (DFG)GermanyCRC - 746
European Communitys Seventh Framework ProgrammeEuropean UnionEDICT - HEALTH-F4-2007-201924

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description