Biological Assembly 1

Protein Symmetry: Asymmetric (View in 3D)

Protein Stoichiometry: Hetero 27-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZ

Macromolecule Content

• Unique protein chains: 29
• Unique nucleic acid chains: 2

3CCE

Structure of Anisomycin resistant 50S Ribosomal Subunit: 23S rRNA mutation U2535A

• DOI: 10.2210/pdb3cce/pdb
• NDB: RR0205

• Classification: RIBOSOME
• Deposited: 2008-02-25 Released: 2008-05-20
• Deposition author(s): Blaha, G., Gurel, G.
• Organism: Haloarcula marismortui

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.232
• R-Value Work: 0.183

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: RIBOSOME

Total Structure Weight: 1493271.88

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
CD	1, 3, O, U, Z	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N	Poseview Image of CD in 3CCE 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)
SR	0, 1, 3, 9, A, B, F, R, S	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N	Poseview Image of SR in 3CCE 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)
K	0	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N	Poseview Image of K in 3CCE 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	0, 3, A, B, J, L, M, N, O, Q, R	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 3CCE 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)
MG	0, 9, A, B, K, T, Y	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N	Poseview Image of MG in 3CCE 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)
NA	0, 9, C, J, M, Q, R, S	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N	Poseview Image of NA in 3CCE 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)

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
1MA	0	RNA LINKING	C11 H16 N5 O7 P		A
OMU	0	RNA LINKING	C10 H15 N2 O9 P		U
OMG	0	RNA LINKING	C11 H16 N5 O8 P		G
UR3	0	RNA LINKING	C10 H15 N2 O9 P		U
PSU	0	RNA LINKING	C9 H13 N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.232
• R-Value Work: 0.183
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 212.83	α = 90.00
b = 299.90	β = 90.00
c = 576.01	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2008-02-25
• Released Date: 2008-05-20
• Deposition author(s): Blaha, G., Gurel, G.

Revision History

• 2011-07-13
  Type: Non-polymer description, Version format compliance
• 2015-05-27
  Type: Source and taxonomy