SMTL ID : 4rh0.1

Spore photoproduct lyase C140A/S76C mutant with bound AdoMet

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x EEM: [(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium(Non-covalent)

EEM.1: 19 residues within 4Å: Chain A: Y.123, C.124, Y.125, A.166, S.169, D.170, V.199, T.200, K.201, S.222, V.259, A.261, P.262, I.297, Q.298, H.299, R.300 Ligands: SO4.7, SF4.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.199 Hydrogen bonds: A:Y.123, A:Y.125, A:D.170, A:D.170, A:V.199, A:K.201, A:S.222, A:A.261, A:R.300, A:R.300 Salt bridges: A:K.201 pi-Stacking: A:Y.123

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

SO4.2: 4 residues within 4Å: Chain A: R.197, R.218, K.255, Q.365 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.365 Water bridges: A:R.218, A:R.218 Salt bridges: A:R.197, A:R.218, A:K.255 SO4.3: 5 residues within 4Å: Chain A: R.95, D.101, T.115, Y.139, T.168 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.95 SO4.4: 5 residues within 4Å: Chain A: G.330, R.331, Y.332, G.333, I.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.331, A:Y.332, A:G.333, A:I.334 SO4.5: 1 residues within 4Å: Chain A: R.63 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.61, A:R.63 SO4.6: 2 residues within 4Å: Chain A: R.72, G.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.71, A:G.73, A:I.74 SO4.7: 11 residues within 4Å: Chain A: Y.123, C.124, Y.125, T.128, R.300, F.301, T.302, A.305, I.309 Ligands: EEM.1, EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.123, A:T.128, A:T.128, A:T.302 Water bridges: A:T.128

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 6 residues within 4Å: Chain A: Y.125, R.300, F.301, T.302, K.336 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.125, A:T.128

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

SF4.9: 7 residues within 4Å: Chain A: C.117, G.119, C.121, C.124, L.126, K.201 Ligands: EEM.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:D.170 Metal complexes: A:C.117, A:C.121, A:C.124, EEM.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benjdia, A. et al., Rescuing DNA repair activity by rewiring the H-atom transfer pathway in the radical SAM enzyme, spore photoproduct lyase. Chem.Commun.(Camb.) (2014)

Release Date

2014-10-22

Peptides

Spore photoproduct lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spore photoproduct lyase

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