1EFR

BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH THE PEPTIDE ANTIBIOTIC EFRAPEPTIN

Structural Biology Knowledgebase: 1EFR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1EFR

Classification: HYDROLASE / ANTIBIOTIC

Total Structure Weight: 355535.41

Macromolecule Entities
Molecule Chains Length Organism Details
BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT ALPHA A, B, C 510 Bos taurus EC#: 3.6.3.14 IUBMB
Mutation: S481G
Gene Name(s): ATP5A1 Gene View ATP5A2
BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT BETA D, E, F 482 Bos taurus EC#: 3.6.3.14 IUBMB
Gene Name(s): ATP5B Gene View
BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT GAMMA G 272 Bos taurus EC#: 3.6.3.14 IUBMB
Gene Name(s): ATP5C1 Gene View ATP5C
EFRAPEPTIN C Q 17 Tolypocladium inflatum

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: F-type ATPase

Protein Name: ATP synthase (F1c10)


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ANP
Query on ANP

A, B, C, F PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

D ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000186 (ACE,TLX,BAL,YCP,LEU,GLY,AIB) Q EFRAPEPTIN C Polypeptide /
Antimicrobial
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.177
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 285.70 α = 90.00
b = 107.40 β = 90.00
c = 139.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-05-24
  • Released Date: 1997-02-12
  • Deposition author(s): Abrahams, J.P., Buchanan, S.K., Van Raaij, M.J., Fearnley, I.M., Leslie, A.G.W., Walker, J.E.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-27
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-27
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-27
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-27
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-27
    Type: Linkage | Details: Linkage
  • 2011-07-27
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-27
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4