1IXF

Crystal Structure of the K intermediate of bacteriorhodopsin

Structural Biology Knowledgebase: 1IXF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.321
  • R-Value Work: 0.291

Literature

Macromolecules
Sequence Display for 1IXF

Classification: PROTON TRANSPORT

Total Structure Weight: 31797.40

Macromolecule Entities
Molecule Chains Length Organism Details
bacteriorhodopsin A 248 Halobacterium salinarum Gene Name(s): bop VNG_1467G
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Bacteriorhodopsin (BR)


Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
L3P
Query on L3P

A 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL- 3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
L2P
Query on L2P

A 2,3-DI-PHYTANYL-GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)- SN-GLYCEROL (Synonym)
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RET
Query on RET

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

A ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.321
  • R-Value Work: 0.291
  • Space Group: P 6 2 2

Unit Cell:

Length (Å) Angle (°)
a = 102.30 α = 90.00
b = 102.30 β = 90.00
c = 112.30 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-20
  • Released Date: 2002-12-18
  • Deposition author(s): Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H., Kouyama, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

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