Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers.

Axelrod, H.L; Abresch, E.C; Paddock, M.L; Okamura, M.Y; Feher, G.

Macromolecule Content

Unique protein chains: 3

1DS8

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

DOI: 10.2210/pdb1ds8/pdb

Classification: PHOTOSYNTHESIS
Deposited: 2000-01-07 Released: 2000-03-08
Deposition author(s): Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.
Organism: Rhodobacter sphaeroides
Mutation(s): 2

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: PHOTOSYNTHESIS

Total Structure Weight: 203764.70

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
Protein Feature View - UniProtKB AC: P0C0Y8 UniProt Full Protein Feature View for P0C0Y8 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P0C0Y8/1DS8
REACTION CENTER PROTEIN M CHAIN	M, S	307	Rhodobacter sphaeroides	Mutation: N307A Gene Name(s): pufM
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P0C0Y9 UniProt Full Protein Feature View for P0C0Y9 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P0C0Y9/1DS8
REACTION CENTER PROTEIN H CHAIN	H, T	260	Rhodobacter sphaeroides	Mutation: G8Q Gene Name(s): puhA
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P0C0Y7 UniProt Full Protein Feature View for P0C0Y7 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P0C0Y7/1DS8

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 & Interactions	3D Interactions
BCL Query on BCL Download SDF File Download CCD File	L, M, R, S	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-RUUWGSCADZ	Poseview Image of BCL in 1DS8 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
BPH Query on BPH Download SDF File Download CCD File	L, M, R, S	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N	Poseview Image of BPH in 1DS8 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
U10 Query on U10 Download SDF File Download CCD File	L, M, R, S	UBIQUINONE-10 Coenzyme Q10 (Synonym) C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N	Poseview Image of U10 in 1DS8 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
LDA Query on LDA Download SDF File Download CCD File	M, S	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N	Poseview Image of LDA in 1DS8 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
CD Query on CD Download SDF File Download CCD File	H, T	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N	Poseview Image of CD in 1DS8 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
FE2 Query on FE2 Download SDF File Download CCD File	M, S	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N	Poseview Image of FE2 in 1DS8 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
CL Query on CL Download SDF File Download CCD File	M, S	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 1DS8 Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	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

Version 1_0: 2000-03-08
Type: Initial release
Version 1_1: 2008-04-27
Type: Version format compliance
Version 1_2: 2011-07-13
Type: Non-polymer description, Version format compliance
Version 1_3: 2011-11-16
Type: Atomic model

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