4FPD

Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway

Structural Biology Knowledgebase: 4FPD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.223

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FPD

Classification: TRANSPORT PROTEIN

Total Structure Weight: 33567.19

Macromolecule Entities
Molecule Chains Length Organism Details
Bacteriorhodopsin A 262 Halobacterium salinarum Mutation: D96G, F171C, F219L
Gene Name(s): bop VNG_1467G

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Bacteriorhodopsin (BR)


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LI1
Query on LI1

A 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]- 2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
LIPID FRAGMENT (Synonym)
C42 H86 O3
YERVUJAKCNBGCR-BIHSMRAKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RET
Query on RET

A RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.223
  • Space Group: P 63
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.93 α = 90.00
b = 60.93 β = 90.00
c = 107.70 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-06-22
  • Released Date: 2013-02-27
  • Deposition author(s): Wang, T., Sessions, A.O., Lunde, C.S., Rouani, S., Glaeser, R.M., Facciotti, M.T., Duan, Y.

Revision History

No revisions since initial release