7W78

Heme exporter HrtBA in complex with Mg-AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

heme exporter complexed with AMPPNP

Nakamura, H.Hisano, T.Rahman, M.M.Tosha, T.Shirouzu, M.Shiro, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ABC transport system, ATP-binding proteinA221Corynebacterium diphtheriae NCTC 13129Mutation(s): 0 
Gene Names: DIP2323
UniProt
Find proteins for Q6NEF2 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NEF2 
Go to UniProtKB:  Q6NEF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NEF2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ABC transport system integral membrane proteinB344Corynebacterium diphtheriae NCTC 13129Mutation(s): 0 
Gene Names: DIP2324
Membrane Entity: Yes 
UniProt
Find proteins for Q6NEF1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NEF1 
Go to UniProtKB:  Q6NEF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NEF1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

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D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MYZ
Query on MYZ

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H [auth B],
I [auth B]
Myristoleic acid
C14 H26 O2
YWWVWXASSLXJHU-WAYWQWQTSA-N
 Ligand Interaction
D12
Query on D12

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J [auth B]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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E [auth A],
F [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.981α = 90
b = 168.981β = 90
c = 94.665γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan26220807
Japan Society for the Promotion of Science (JSPS)Japan16K07309
Japan Society for the Promotion of Science (JSPS)JapanJP19H00926
Japan Society for the Promotion of Science (JSPS)JapanJP19H05761

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release