SMTL ID : 2h5l.2 (1 other biounit)

S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: T.156, T.157, T.158, N.190, C.194, G.219, G.221, D.222, V.223, T.241, E.242, I.243, D.244, N.247, T.274, T.275, C.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Chain B: L.408, Q.412, L.416, K.425, Y.429 Ligands: 3DD.2 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.223 Hydrogen bonds: A:T.157, A:T.157, A:T.158, A:T.158, A:T.158, A:N.190, A:D.222, A:V.223, A:T.241, A:I.243, A:D.244, A:N.247, A:H.300, A:N.345, A:N.345, B:Q.412, B:K.425, B:K.425, B:Y.429, B:Y.429 Water bridges: A:D.222, A:F.301 NAD.3: 30 residues within 4Å: Chain A: L.408, Q.412, L.416, K.425, Y.429 Chain B: T.156, T.157, T.158, N.190, C.194, G.219, G.221, D.222, V.223, T.241, E.242, I.243, D.244, N.247, T.274, T.275, C.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Ligands: 3DD.4 21 PLIP interactions: 4 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:Q.412, A:K.425, A:K.425, A:Y.429, B:T.157, B:T.157, B:T.158, B:T.158, B:N.190, B:D.222, B:V.223, B:I.243, B:D.244, B:N.247, B:T.275, B:H.300, B:N.345, B:N.345 Hydrophobic interactions: B:V.223 Water bridges: B:T.158, B:T.158 NAD.5: 30 residues within 4Å: Chain C: T.156, T.157, T.158, N.190, C.194, G.219, G.221, D.222, V.223, T.241, E.242, I.243, D.244, N.247, T.274, T.275, C.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Chain D: L.408, Q.412, L.416, K.425, Y.429 Ligands: 3DD.6 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:V.223 Hydrogen bonds: C:T.157, C:T.157, C:T.157, C:T.158, C:N.190, C:D.222, C:V.223, C:I.243, C:D.244, C:N.247, C:T.275, C:H.300, C:N.345, C:N.345, D:Q.412, D:K.425, D:K.425, D:Y.429 NAD.7: 31 residues within 4Å: Chain C: L.408, Q.412, L.416, K.425, Y.429 Chain D: T.156, T.157, T.158, N.190, C.194, G.219, G.221, D.222, V.223, T.241, E.242, I.243, D.244, N.247, T.274, T.275, G.276, C.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Ligands: 3DD.8 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.223 Hydrogen bonds: D:T.157, D:T.157, D:T.157, D:T.158, D:T.158, D:N.190, D:D.222, D:V.223, D:T.241, D:I.243, D:D.244, D:N.247, D:H.300, D:N.345, D:N.345, C:Q.412, C:K.425, C:K.425, C:Y.429, C:Y.429

4 x 3DD: (2R,3R)-4-(4-AMINO-1H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-2,3-DIHYDROXYBUTANOIC ACID(Non-covalent)

3DD.2: 17 residues within 4Å: Chain A: L.53, H.54, T.56, E.58, T.59, D.130, E.155, T.156, K.185, D.189, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.53 Hydrogen bonds: A:H.54, A:E.58, A:E.58, A:T.59, A:T.156, A:T.156, A:H.352 Salt bridges: A:K.185 3DD.4: 17 residues within 4Å: Chain B: L.53, H.54, T.56, E.58, T.59, D.130, E.155, T.156, K.185, D.189, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.53 Hydrogen bonds: B:H.54, B:T.56, B:E.58, B:T.156, B:H.352 Salt bridges: B:K.185 3DD.6: 17 residues within 4Å: Chain C: L.53, H.54, T.56, E.58, T.59, D.130, E.155, T.156, K.185, D.189, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.53 Hydrogen bonds: C:H.54, C:T.56, C:E.58, C:T.156, C:H.352 Salt bridges: C:K.185 3DD.8: 17 residues within 4Å: Chain D: L.53, H.54, T.56, E.58, T.59, D.130, E.155, T.156, K.185, D.189, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAD.7 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.53 Hydrogen bonds: D:H.54, D:E.58, D:E.58, D:T.59, D:T.156, D:T.156, D:H.352 Salt bridges: D:K.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, T. et al., Structure and function of eritadenine and its 3-deaza analogues: Potent inhibitors of S-adenosylhomocysteine hydrolase and hypocholesterolemic agents. Biochem.Pharm. (2007)

Release Date

2007-04-10

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Adenosylhomocysteinase

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