1E12

Halorhodopsin, a light-driven chloride pump

Structural Biology Knowledgebase: 1E12 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.237

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1E12

Classification: TRANSPORT PROTEIN

Total Structure Weight: 31127.64

Macromolecule Entities
Molecule Chains Length Organism Details
HALORHODOPSIN A 253 Halobacterium salinarum Mutation: V229A
Details: SCHIFF BASE LINKAGE BETWEEN LYS A242 (NZ) AND RET A999 (C15)
Gene Name(s): hop VNG_0180G

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Halorhodopsin (HR)


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-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)
PLM
Query on PLM

A PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-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: 1.8 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.237
  • Space Group: P 63 2 2

Unit Cell:

Length (Å) Angle (°)
a = 67.30 α = 90.00
b = 67.30 β = 90.00
c = 209.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-04-14
  • Released Date: 2000-06-02
  • Deposition author(s): Essen, L.-O., Kolbe, M., Oesterhelt, D.

Revision History

  • 2016-02-03
    Type: Refinement description | Details: REMARK 3
  • 2016-02-03
    Type: Linkage | Details: CONECT
  • 2016-02-03
    Type: Non-polymer description | Details: HETSYN, FORMUL, REMARK 620, HETNAM, HET
  • 2016-02-03
    Type: Citation | Details: REMARK 1, JRNL
  • 2016-02-03
    Type: Other | Details: SCALE2, REMARK 610, REMARK 615
  • 2016-02-03
    Type: Source and taxonomy | Details: SOURCE
  • 2016-02-03
    Type: Atom nomenclature | Details: HETATM
  • 2016-02-03
    Type: Function and keywords | Details: KEYWDS
  • 2016-02-03
    Type: Polymer description | Details: COMPND
  • 2016-02-03
    Type: Sequence database correspondence | Details: DBREF, SEQADV
  • 2016-02-03
    Type: Binding sites and description | Details: REMARK 800, SITE
  • 2012-11-14
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2012-11-14
    Type: Sequence database correspondence | Details: DBREF
  • 2012-11-14
    Type: Secondary structure | Details: HELIX
  • 2012-11-14
    Type: Version format compliance | Details: REMARK 4
  • 2012-11-14
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2012-11-14
    Type: Atom nomenclature | Details: HETATM
  • 2012-11-14
    Type: Other | Details: REMARK 375,REMARK 465,REMARK 610,REMARK 615,REMARK 525,REMARK 280
  • 2012-11-14
    Type: Refinement description | Details: REMARK 3
  • 2012-11-14
    Type: Geometry validation | Details: REMARK 500
  • 2012-11-14
    Type: Non-polymer description | Details: HETSYN,FORMUL,HET