2WPD

THE MG.ADP INHIBITED STATE OF THE YEAST F1C10 ATP SYNTHASE

Structural Biology Knowledgebase: 2WPD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.297
  • R-Value Work: 0.286

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2WPD

Classification: HYDROLASE

Total Structure Weight: 450532.59

Macromolecule Entities
Molecule Chains Length Organism Details
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL A, B, C 510 Saccharomyces cerevisiae Gene Name(s): ATP1 YBL099W YBL0827
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL D, E, F 478 Saccharomyces cerevisiae EC#: 3.6.3.14 IUBMB
Gene Name(s): ATP2 YJR121W J2041
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL G 278 Saccharomyces cerevisiae Gene Name(s): ATP3 ATP3a ATP3b YBR039W YBR0408
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL H 138 Saccharomyces cerevisiae Gene Name(s): ATP16 YDL004W D2935 YD8119.03
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL I 61 Saccharomyces cerevisiae Fragment: RESIDUES 2-62
Gene Name(s): ATP15 YPL271W P0345
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL J, K, L..., M, N, O, P, Q, R, SJ, K, L, M, N, O, P, Q, R, S 76 Saccharomyces cerevisiae EC#: 3.6.3.14 IUBMB
Gene Name(s): OLI1 ATP9 OLI3 PHO2 Q0130
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: F-type ATPase

Protein Name: F1-c-ring (c10) complex


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

A, B, C ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

D, F 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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.297
  • R-Value Work: 0.286
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 134.99 α = 90.00
b = 173.94 β = 92.69
c = 137.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-08-05
  • Released Date: 2010-07-07
  • Deposition author(s): Dautant, A., Velours, J., Giraud, M.-F.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4