SMTL ID : 3wv9.3 (7 other biounits)

Guanylylpyridinol (GP)- and ATP-bound HcgE from Methanothermobacter marburgensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 14 residues within 4Å: Chain A: V.19, G.20, G.22, R.23, I.46, D.47, Q.49, K.69, Y.91, I.92, I.109, A.110, I.117 Ligands: FEG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.22, A:R.23, A:Q.49, A:Q.49, A:Q.49, A:K.69, A:K.69, A:I.92, A:I.92, A:A.110 Salt bridges: A:R.23, A:R.23, A:K.69

1 x FEG: 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine(Non-covalent)

FEG.2: 17 residues within 4Å: Chain A: L.24, I.109, A.110, G.112, D.113, T.114, L.115, T.135, G.137, V.138, F.139, P.159, I.160, K.179, I.181, R.182 Ligands: ATP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.24, A:A.110, A:V.138, A:F.139 Hydrogen bonds: A:G.112, A:D.113, A:T.114, A:T.135, A:G.137, A:V.138, A:I.181, A:R.182

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: F.81, S.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.81 SO4.4: 2 residues within 4Å: Chain A: Y.124, R.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.124 Salt bridges: A:R.128 SO4.5: 1 residues within 4Å: Chain A: E.120 No protein-ligand interaction detected (PLIP) SO4.6: 1 residues within 4Å: Chain A: R.59 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujishiro, T. et al., Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor. Nat Commun (2015)

Release Date

2015-04-29

Peptides

Hmd co-occurring protein HcgE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Hmd co-occurring protein HcgE

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