1DS8

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

Structural Biology Knowledgebase: 1DS8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.227

Literature

Macromolecules
Sequence Display for 1DS8

Classification: PHOTOSYNTHESIS

Total Structure Weight: 203766.44

Macromolecule Entities
Molecule Chains Length Organism Details
REACTION CENTER PROTEIN L CHAIN L, R 281 Rhodobacter sphaeroides Gene Name(s): pufL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
REACTION CENTER PROTEIN M CHAIN M, S 307 Rhodobacter sphaeroides Mutation: N307A
Gene Name(s): pufM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
REACTION CENTER PROTEIN H CHAIN H, T 260 Rhodobacter sphaeroides Mutation: G8Q
Gene Name(s): puhA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Photosynthetic Reaction Centers

Protein Name: Photosynthetic Reaction Center


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BCL
Query on BCL

L, M, R, S BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BPH
Query on BPH

L, M, R, S BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
U10
Query on U10

L, M, R, S UBIQUINONE-10
Coenzyme Q10 (Synonym)
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LDA
Query on LDA

M, S LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

H, T CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

M, S FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

M, S CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 0.256
  • R-Value Work: 0.227
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 139.59 α = 90.00
b = 139.59 β = 90.00
c = 272.86 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-01-07
  • Released Date: 2000-03-08
  • Deposition author(s): Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4