Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b.

Volbeda, A; Darnault, C; Parkin, A; Sargent, F; Armstrong, F.A; Fontecilla-Camps, J.C.

Macromolecule Content

Unique protein chains: 3

4GD3

Structure of E. coli hydrogenase-1 in complex with cytochrome b

DOI: 10.2210/pdb4gd3/pdb

Classification: OXIDOREDUCTASE / ELECTRON TRANSPORT
Deposited: 2012-07-31 Released: 2013-01-02
Deposition author(s): Volbeda, A., Fontecilla-Camps, J.C., Darnault, C.
Organism: Escherichia coli
Expression System: Escherichia coli
Mutation(s): 1

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.3 Å
R-Value Free: 0.236
R-Value Work: 0.200

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: OXIDOREDUCTASE / ELECTRON TRANSPORT

Total Structure Weight: 470137.84

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
Hydrogenase-1 small chain	Q, R, S, T	335	Escherichia coli	EC#: 1.12.99.6 IUBMB Mutation: P242C Gene Name(s): hyaA b0972 JW0954
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P69739 UniProt Full Protein Feature View for P69739 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P69739/4GD3
Hydrogenase-1 large chain	J, K, L, M	582	Escherichia coli	EC#: 1.12.99.6 IUBMB Gene Name(s): hyaB b0973 JW0955
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P0ACD8 UniProt Full Protein Feature View for P0ACD8 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P0ACD8/4GD3
Ni/Fe-hydrogenase 1 B-type cytochrome subunit	A, B	235	Escherichia coli	Gene Name(s): hyaC b0974 JW0956
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P0AAM1 UniProt Full Protein Feature View for P0AAM1 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P0AAM1/4GD3

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Oxidoreductases

Protein Name: O₂-tolerant Hydrogenase-1 in complex with cytochrome b

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
HEM Query on HEM Download SDF File Download CCD File	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME (Synonym) C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L	Poseview Image of HEM in 4GD3 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)
LMT Query on LMT Download SDF File Download CCD File	A, B, R, T	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N	Poseview Image of LMT in 4GD3 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 Query on SF4 Download SDF File Download CCD File	Q, R, S, T	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-VKOJMFJBAC	Poseview Image of SF4 in 4GD3 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)
F4S Query on F4S Download SDF File Download CCD File	Q, R, S, T	FE4-S3 CLUSTER T-CLUSTER (Synonym) Fe₄ S₃ QQACTBFBZNWJMV-UHFFFAOYSA-N	Poseview Image of F4S in 4GD3 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)
FCO Query on FCO Download SDF File Download CCD File	J, K, L, M	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N	Poseview Image of FCO in 4GD3 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)
NI Query on NI Download SDF File Download CCD File	J, K, L, M	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N	Poseview Image of NI in 4GD3 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	J, K, L, M, Q, S	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M	Poseview Image of CL in 4GD3 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 Query on MG Download SDF File Download CCD File	J, K, L, M	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N	Poseview Image of MG in 4GD3 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)