SMTL ID : 1xwf.1

K185N mutated S-adenosylhomocysteine hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: T.157, 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: Q.412, K.425, Y.429 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.223 Hydrogen bonds: A:T.157, A:T.157, A:D.222, A:V.223, A:I.243, A:D.244, A:N.247, A:T.275, A:G.299, A:N.345, B:Q.412, B:Q.412, B:K.425, B:K.425, B:Y.429 Salt bridges: B:K.425 NAD.3: 28 residues within 4Å: Chain A: Q.412, K.425, Y.429 Chain B: T.157, 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 Ligands: ADN.4 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.157, B:T.157, B:D.222, B:V.223, B:E.242, B:I.243, B:D.244, B:N.247, B:T.275, B:G.299, B:N.345, A:Q.412, A:Q.412, A:K.425, A:K.425, A:Y.429 Water bridges: B:H.300 NAD.5: 29 residues within 4Å: Chain C: T.157, 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 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:V.223 Hydrogen bonds: C:T.157, C:T.157, C:D.222, C:V.223, C:I.243, C:D.244, C:N.247, C:T.275, C:G.299, C:N.345, D:Q.412, D:Q.412, D:K.425, D:K.425, D:Y.429, D:Y.429 Salt bridges: D:K.425 NAD.7: 28 residues within 4Å: Chain C: L.408, Q.412, K.425, Y.429 Chain D: T.157, 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 19 PLIP interactions: 12 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:V.223 Hydrogen bonds: D:T.157, D:T.157, D:D.222, D:V.223, D:I.243, D:D.244, D:N.247, D:T.275, D:G.299, D:N.345, C:Q.412, C:Q.412, C:K.425, C:K.425, C:Y.429, C:Y.429 Water bridges: D:T.157 Salt bridges: C:K.425

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 16 residues within 4Å: Chain A: L.53, H.54, T.56, E.58, T.59, D.130, E.155, D.189, H.300, L.343, L.346, M.350, G.351, H.352, M.357, F.361 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.58, A:E.58, A:D.189, A:H.300, A:H.352 ADN.4: 17 residues within 4Å: Chain B: L.53, H.54, T.56, E.58, T.59, D.130, E.155, D.189, H.300, L.343, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.56, B:E.58, B:E.58, B:D.189, B:H.300, B:H.352 ADN.6: 16 residues within 4Å: Chain C: L.53, H.54, T.56, E.58, T.59, D.130, E.155, D.189, H.300, L.343, L.346, M.350, G.351, H.352, M.357, F.361 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.58, C:E.155, C:D.189, C:H.300, C:H.352 ADN.8: 16 residues within 4Å: Chain D: L.53, H.54, T.56, E.58, T.59, D.130, E.155, D.189, H.300, L.343, L.346, M.350, G.351, H.352, M.357, F.361 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.58, D:E.155, D:D.189, D:H.300, D:H.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, T. et al., Catalytic mechanism of S-adenosylhomocysteine hydrolase: Roles of His 54, Asp130, Glu155, Lys185, and Aspl89. Int.J.Biochem.Cell Biol. (2005)

Release Date

2005-09-20

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase