SMTL ID : 3wvc.1

Guanylylpyridinol (GP)-bound HcgF from Methanocaldococcus jannaschii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: S.59, I.60, I.61, K.82 Chain B: R.50 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.60, A:I.61 Water bridges: A:K.82, A:K.82 Salt bridges: A:K.82, B:R.50 SO4.2: 3 residues within 4Å: Chain A: K.156, K.159, R.160 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.159, A:R.160 SO4.5: 5 residues within 4Å: Chain A: R.50 Chain B: S.59, I.60, I.61, K.82 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.59, B:I.60, B:I.61 Water bridges: B:K.82 Salt bridges: B:K.82, A:R.50 SO4.6: 3 residues within 4Å: Chain B: F.132, K.156, R.160 5 PLIP interactions: 5 interactions with chain B Water bridges: B:T.133, B:K.156, B:R.160 Salt bridges: B:K.156, B:R.160 SO4.7: 2 residues within 4Å: Chain B: K.94, R.129 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.129 Salt bridges: B:K.94, B:R.129 SO4.8: 3 residues within 4Å: Chain B: H.3, M.4, R.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.4 Salt bridges: B:H.3, B:R.50

1 x ZGP: 5'-O-[(R)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxo-2-sulfanylethyl)pyridin-4-yl]oxy}phosphoryl]guanosine(Covalent)

ZGP.3: 14 residues within 4Å: Chain A: C.12, F.13, H.15, T.113, A.114, L.140, F.143, I.146, R.149 Chain B: H.23, A.27, G.28, Y.29, E.30 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.13, A:L.140, A:I.146 Hydrogen bonds: A:F.13, A:T.113, A:A.114, A:R.149, B:Y.29, B:E.30 Salt bridges: A:H.15, B:H.23, B:E.30 pi-Stacking: B:Y.29, B:Y.29

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

FEG.4: 15 residues within 4Å: Chain A: H.23, A.27, G.28, Y.29, E.30 Chain B: C.12, F.13, H.15, P.58, T.113, A.114, L.140, F.143, I.146, R.149 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:A.27, A:E.30, B:F.13, B:T.113, B:A.114, B:A.114, B:R.149 Water bridges: A:G.28, A:E.30, A:D.31 Salt bridges: A:H.23, A:E.30, B:H.15 pi-Stacking: A:Y.29, A:Y.29 Hydrophobic interactions: B:F.13, B:P.58, B:L.140, B:I.146

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

UPF0254 protein MJ1251: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UPF0254 protein MJ1251

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