SMTL ID : 1ky5.1

D244E mutant S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 29 residues within 4Å: Chain A: T.156, T.157, T.158, D.189, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.244, N.247, T.274, T.275, G.276, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Chain B: L.408, Q.412, K.425, Y.429 Ligands: ADY.2 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:N.190, A:V.223 Hydrogen bonds: A:T.157, A:T.158, A:T.158, A:N.190, A:D.222, A:V.223, A:I.243, A:H.300, A:N.345, A:N.345, B:Q.412, B:K.425, B:K.425, B:Y.429, B:Y.429 Salt bridges: B:K.425 NAI.3: 28 residues within 4Å: Chain A: Q.412, K.425, Y.429 Chain B: T.156, T.157, T.158, D.189, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.244, N.247, T.274, T.275, G.276, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Ligands: ADY.4 20 PLIP interactions: 5 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:Q.412, A:K.425, A:K.425, A:Y.429, A:Y.429, B:T.157, B:T.158, B:T.158, B:T.158, B:N.190, B:D.222, B:V.223, B:I.243, B:H.300, B:N.345, B:N.345 Hydrophobic interactions: B:N.190, B:V.223 Water bridges: B:S.186, B:S.186 NAI.5: 30 residues within 4Å: Chain C: T.156, T.157, T.158, D.189, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.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 Chain D: L.408, Q.412, K.425, Y.429 Ligands: ADY.6 20 PLIP interactions: 13 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:V.223 Hydrogen bonds: C:T.158, C:T.158, C:T.158, C:N.190, C:D.222, C:V.223, C:I.243, C:H.300, C:N.345, C:N.345, D:Q.412, D:K.425, D:K.425, D:Y.429, D:Y.429, D:Y.429 Water bridges: C:S.186, C:S.186 Salt bridges: D:K.425 NAI.7: 29 residues within 4Å: Chain C: L.408, Q.412, K.425, Y.429 Chain D: T.156, T.157, T.158, D.189, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.244, N.247, T.274, T.275, G.276, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Ligands: ADY.8 22 PLIP interactions: 15 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:V.223 Hydrogen bonds: D:T.157, D:T.158, D:T.158, D:T.158, D:N.190, D:D.222, D:V.223, D:T.241, D:I.243, D:H.300, D:N.345, D:N.345, C:Q.412, C:K.425, C:K.425, C:Y.429, C:Y.429, C:Y.429 Water bridges: D:G.276, D:G.276 Salt bridges: C:K.425

4 x ADY: 3'-OXO-ADENOSINE(Non-covalent)

ADY.2: 19 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, H.300, L.343, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAI.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.56, A:E.58, A:E.58, A:T.59, A:K.185, A:K.185, A:H.300, A:H.352 ADY.4: 18 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, H.300, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAI.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.56, B:E.58, B:E.58, B:T.59, B:T.156, B:K.185, B:D.189, B:H.300, B:H.352 ADY.6: 19 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, H.300, L.343, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAI.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.58, C:E.155, C:T.156, C:K.185, C:K.185, C:H.300, C:H.352 ADY.8: 19 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, H.300, L.343, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAI.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.56, D:E.58, D:E.155, D:T.156, D:K.185, D:K.185, D:H.300, D:H.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takata, Y. et al., Catalytic Mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190. J.Biol.Chem. (2002)

Release Date

2002-09-25

Peptides

S-adenosylhomocysteine hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

S-adenosylhomocysteine hydrolase

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