SMTL ID : 3wv9.8 (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

homo-trimer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: V.19, G.20, A.21, G.22, R.23, I.46, D.47, Q.49, D.54, D.55, K.69, Y.91, I.92, E.108, I.109, A.110 Chain C: H.36 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.23, A:Q.49, A:Q.49, A:Q.49, A:S.52, A:S.52, A:D.54, A:D.54, A:K.69, A:I.92, A:I.92, A:A.110 Salt bridges: A:R.23, A:R.23, A:R.23, A:K.69, A:K.69, C:H.36 pi-Stacking: A:Y.91, A:Y.91 ATP.3: 17 residues within 4Å: Chain A: H.36 Chain B: V.19, G.20, A.21, G.22, R.23, I.46, D.47, Q.49, D.54, D.55, K.69, Y.91, I.92, E.108, I.109, A.110 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.23, B:Q.49, B:Q.49, B:Q.49, B:S.52, B:S.52, B:D.54, B:D.54, B:K.69, B:I.92, B:I.92, B:A.110 Salt bridges: B:R.23, B:R.23, B:R.23, B:K.69, B:K.69, A:H.36 pi-Stacking: B:Y.91, B:Y.91 ATP.5: 17 residues within 4Å: Chain B: H.36 Chain C: V.19, G.20, A.21, G.22, R.23, I.46, D.47, Q.49, D.54, D.55, K.69, Y.91, I.92, E.108, I.109, A.110 20 PLIP interactions: 1 interactions with chain B, 19 interactions with chain C Salt bridges: B:H.36, C:R.23, C:R.23, C:R.23, C:K.69, C:K.69 Hydrogen bonds: C:R.23, C:Q.49, C:Q.49, C:Q.49, C:S.52, C:S.52, C:D.54, C:D.54, C:K.69, C:I.92, C:I.92, C:A.110 pi-Stacking: C:Y.91, C:Y.91

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

SO4.2: 2 residues within 4Å: Chain A: K.50, Y.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.68, A:Y.68 Salt bridges: A:K.50 SO4.4: 2 residues within 4Å: Chain B: K.50, Y.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.68, B:Y.68 Salt bridges: B:K.50 SO4.6: 2 residues within 4Å: Chain C: K.50, Y.68 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.68, C:Y.68 Salt bridges: C:K.50

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
D

C
D

Hmd co-occurring protein HcgE

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