SMTL ID : 1ky4.1

S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints

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: 28 residues within 4Å: Chain A: D.189, 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 Chain B: L.408, Q.412, L.416, K.425, Y.429 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.222, A:V.223, A:I.243, A:D.244, A:N.345, A:N.345, B:Q.412, B:K.425, B:K.425, B:Y.429 Water bridges: A:T.157, A:T.157, A:H.300, B:Q.412 NAD.2: 29 residues within 4Å: Chain A: T.406, L.408, Q.412, L.416, K.425, Y.429 Chain B: D.189, 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 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.222, B:V.223, B:I.243, B:D.244, B:N.345, B:N.345, A:T.406, A:Q.412, A:Q.412, A:K.425, A:K.425, A:Y.429 Water bridges: B:G.221, B:G.221 NAD.3: 28 residues within 4Å: Chain C: D.189, 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 Chain D: L.408, Q.412, L.416, K.425, Y.429 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:Q.412, D:Q.412, D:K.425, D:K.425, D:Y.429, D:Y.429, C:D.222, C:V.223, C:I.243, C:D.244, C:T.275, C:N.345, C:N.345 NAD.4: 27 residues within 4Å: Chain C: Q.412, L.416, K.425, Y.429 Chain D: D.189, 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 15 PLIP interactions: 9 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:D.222, D:V.223, D:I.243, D:D.244, D:T.275, D:N.345, D:N.345, C:Q.412, C:K.425, C:K.425, C:Y.429, C:Y.429 Water bridges: D:G.221, D:G.221, C:Q.412

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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