1DZE

STRUCTURE OF THE M INTERMEDIATE OF BACTERIORHODOPSIN TRAPPED AT 100K

Structural Biology Knowledgebase: 1DZE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.257

Literature

Macromolecules
Sequence Display for 1DZE

Classification: BACTERIORHODOPSIN

Total Structure Weight: 31335.37

Macromolecule Entities
Molecule Chains Length Organism Details
BACTERIORHODOPSIN (M INTERMEDIATE) A 248 Halobacterium salinarum Details: 5 LIPIDS AND 18 WATER MOLECULES
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 8 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)
L4P
Query on L4P

A 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL- 3'-SN-GLYCEROL (Synonym)
C46 H95 O8 P
AFYVWQWWQKSZEV-WGOBCRBGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
L1P
Query on L1P

A 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)- SN-GLYCERO-3-PHOSPHATE (Synonym)
C43 H89 O6 P
UKQGAMWGTOTQPC-ALOLAALWSA-N
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: 2.5 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.257
  • Space Group: P 6 2 2

Unit Cell:

Length (Å) Angle (°)
a = 102.40 α = 90.00
b = 102.40 β = 90.00
c = 112.30 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-02-25
  • Released Date: 2000-08-16
  • Deposition author(s): Takeda, K., Matsui, Y., Sato, H., Hino, T., Kanamori, E., Okumura, H., Yamane, T., Iizuka, T., Kamiya, N., Adachi, S., Kouyama, T.

Revision History

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