SMTL ID : 7r3a.1 (3 other biounits)

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Methanococcus maripaludis in complex with inosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

2 x NOS: INOSINE(Non-covalent)

NOS.1: 18 residues within 4Å: Chain A: H.70, E.72, K.74, T.75, D.143, E.168, T.169, K.198, D.202, H.313, L.355, L.358, D.362, G.363, H.364, M.369, F.373 Ligands: NAD.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.72, A:K.74, A:T.75, A:E.168, A:K.198, A:H.313, A:H.364 NOS.5: 18 residues within 4Å: Chain B: H.70, E.72, K.74, T.75, D.143, E.168, T.169, K.198, D.202, H.313, L.355, L.358, D.362, G.363, H.364, M.369, F.373 Ligands: NAD.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.72, B:K.74, B:T.75, B:T.169, B:T.169, B:K.198, B:H.313, B:N.357, B:H.364

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 30 residues within 4Å: Chain A: T.169, T.170, T.171, D.202, N.203, T.207, G.232, G.234, W.235, C.236, T.254, E.255, V.256, N.257, R.260, T.287, T.288, G.289, C.290, I.293, A.311, G.312, H.313, L.355, N.357, L.358, H.364 Chain B: L.420, Q.424 Ligands: NOS.1 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.170, A:T.170, A:T.170, A:T.171, A:N.203, A:G.234, A:W.235, A:C.236, A:V.256, A:N.257, A:R.260, A:R.260, A:H.313, A:N.357, A:N.357, B:Q.424 Salt bridges: A:R.260 NAD.6: 30 residues within 4Å: Chain A: L.420, Q.424 Chain B: T.169, T.170, T.171, D.202, N.203, T.207, G.232, Y.233, G.234, W.235, C.236, T.254, E.255, V.256, N.257, R.260, T.287, T.288, G.289, C.290, I.293, A.311, G.312, H.313, L.355, N.357, H.364 Ligands: NOS.5 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.203, B:T.207 Hydrogen bonds: B:T.170, B:T.170, B:T.171, B:T.171, B:N.203, B:G.234, B:W.235, B:C.236, B:V.256, B:R.260, B:R.260, B:H.313, B:N.357, B:N.357, A:Q.424, A:Q.424 Salt bridges: B:R.260

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: W.235, R.238, N.257, R.260, E.263 Chain B: Y.196, Y.399 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.257, A:R.260, B:Y.399 PG4.4: 9 residues within 4Å: Chain A: Y.196, L.200, Y.399 Chain B: W.235, R.238, N.257, I.259, R.260, E.263 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.257, B:R.260, A:Y.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saleem-Batcha, R. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with inosine. To Be Published

Release Date

2023-02-15

Peptides

S-inosyl-L-homocysteine hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

S-inosyl-L-homocysteine hydrolase

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