Biological Assembly 1

Protein Symmetry: Cyclic - C3 (View in 3D)

Protein Stoichiometry: Hetero 9-mer - A3B3C3

Macromolecule Content

• Unique protein chains: 3

1KQG

FORMATE DEHYDROGENASE N FROM E. COLI

• DOI: 10.2210/pdb1kqg/pdb

• Classification: OXIDOREDUCTASE
• Deposited: 2002-01-05 Released: 2002-03-15
• Deposition author(s): Jormakka, M., Tornroth, S., Byrne, B., Iwata, S.
• Organism: Escherichia coli

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.239
• R-Value Work: 0.198

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: OXIDOREDUCTASE

Total Structure Weight: 177065.08

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex II

Protein Name: Formate dehydrogenase-N

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
CDL	B	CARDIOLIPIN 3'-SN-GLYCEROL, (Synonym) C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L	Poseview Image of CDL in 1KQG 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)
MGD	A	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9- TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 4-ONE GUANOSINE DINUCLEOTIDE MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE (Synonym) C20 H26 N10 O13 P2 S2 VQAGYJCYOLHZDH-ILXWUORBSA-N	Poseview Image of MGD in 1KQG 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)
HEM	C	PROTOPORPHYRIN IX CONTAINING FE HEME (Synonym) C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L	Poseview Image of HEM in 1KQG 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)
SF4	A, B	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC	Poseview Image of SF4 in 1KQG 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)
HQO	C	2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE 2-HEPTYL-1-OXY-QUINOLIN-4-OL (Synonym) C16 H21 N O2 NZPACTGCRWDXCJ-UHFFFAOYSA-N	Poseview Image of HQO in 1KQG 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)
6MO	A	MOLYBDENUM(VI) ION Mo HCNGUXXTNNIKCQ-UHFFFAOYSA-N	Poseview Image of 6MO in 1KQG 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 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEC		L-PEPTIDE LINKING	C3 H7 N O2 Se		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.239
• R-Value Work: 0.198
• Space Group: P 2₁ 3

Unit Cell:

Length (Å)	Angle (°)
a = 203.00	α = 90.00
b = 203.00	β = 90.00
c = 203.00	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

• Deposited Date: 2002-01-05
• Released Date: 2002-03-15
• Deposition author(s): Jormakka, M., Tornroth, S., Byrne, B., Iwata, S.

Revision History

• 2008-04-02
  Type: Version format compliance
• 2011-07-13
  Type: Derived calculations, Version format compliance
• 2014-02-19
  Type: Atomic model, Structure summary
• 2014-08-06
  Type: Derived calculations, Structure summary