Biological Assembly 1

Protein Symmetry: Cyclic - C2 (View in 3D)

Protein Stoichiometry: Hetero 4-mer - A2B2

Biological Assembly 2

Protein Symmetry: C1 (View in 3D)

Protein Stoichiometry: AB

Macromolecule Content

• Unique protein chains: 2

5IMT

Toxin receptor complex

• DOI: 10.2210/pdb5imt/pdb

• Classification: TOXIN
• Deposited: 2016-03-06 Released: 2016-08-24
• Deposition author(s): Morton, C.J., Lawrence, S.L., Feil, S.C., Parker, M.W.
• Organism: Streptococcus intermedius | Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 5

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.257
• R-Value Work: 0.208

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: TOXIN

Total Structure Weight: 68885.16

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
PGE	A	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N	Poseview Image of PGE in 5IMT 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)
SO4	A, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L	Poseview Image of SO4 in 5IMT 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)
ZN	A, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N	Poseview Image of ZN in 5IMT 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)
CU	A	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N	Poseview Image of CU in 5IMT 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: 2.7 Å
• R-Value Free: 0.257
• R-Value Work: 0.208
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 93.73	α = 90.00
b = 166.56	β = 90.00
c = 118.25	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2016-03-06
• Released Date: 2016-08-24
• Deposition author(s): Morton, C.J., Lawrence, S.L., Feil, S.C., Parker, M.W.

Revision History

• 2016-09-14
  Type: Database references