SMTL ID : 3zfs.1

Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-functional Binders)

FCO.1: 1 residues within 4Å: Ligands: NI.2 Protein-ligand interaction information (PLIP) not available

1 x NI: NICKEL (II) ION(Non-functional Binders)

NI.2: 1 residues within 4Å: Ligands: FCO.1 Protein-ligand interaction information (PLIP) not available

1 x FE2: FE (II) ION(Non-covalent)

FE2.3: 1 residues within 4Å: Chain A: A.347 Protein-ligand interaction information (PLIP) not available

4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.4: 7 residues within 4Å: Chain B: G.56, C.57, G.59, G.130, S.131, C.132, C.171 Protein-ligand interaction information (PLIP) not available SF4.5: 6 residues within 4Å: Chain B: C.249, K.251, C.252, G.253, I.254, C.255 Protein-ligand interaction information (PLIP) not available SF4.6: 6 residues within 4Å: Chain B: I.221, G.222, C.223, G.224, T.225, C.226 Protein-ligand interaction information (PLIP) not available SF4.8: 4 residues within 4Å: Chain C: P.103, C.104, C.134, M.135 Protein-ligand interaction information (PLIP) not available

1 x F42: COENZYME F420(Non-covalent)

F42.7: 5 residues within 4Å: Chain C: G.164, S.209, V.210, S.217 Ligands: FAD.9 Protein-ligand interaction information (PLIP) not available

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.9: 14 residues within 4Å: Chain C: Q.24, D.25, G.26, I.28, V.29, V.47, A.48, A.72, T.74, Y.76, I.132, G.208, S.209 Ligands: F42.7 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mills, D.J. et al., De Novo Modeling of the F420-Reducing [Nife]-Hydrogenase from a Methanogenic Archaeon by Cryo-Electron Microscopy. Elife (2013)

Release Date

2013-03-06

Peptides

F420-REDUCING HYDROGENASE, SUBUNIT ALPHA: A
F420-REDUCING HYDROGENASE, SUBUNIT GAMMA: B
F420-REDUCING HYDROGENASE, SUBUNIT BETA: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

F420-REDUCING HYDROGENASE, SUBUNIT ALPHA

F420-REDUCING HYDROGENASE, SUBUNIT GAMMA

F420-REDUCING HYDROGENASE, SUBUNIT BETA

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