SMTL ID : 1d4f.1

CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT 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: 25 residues within 4Å: Chain A: T.156, T.157, T.158, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.244, N.247, T.275, C.277, I.280, I.298, H.300, L.343, N.345, H.352 Chain B: L.408, Q.412, Y.429 Ligands: ADN.2 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.223 Hydrogen bonds: A:T.156, A:T.157, A:T.158, A:T.158, A:N.190, A:D.222, A:D.222, A:V.223, A:E.242, A:H.300, A:H.300, A:N.345, A:N.345, B:Q.412, B:Y.429 NAD.3: 26 residues within 4Å: Chain A: L.408, Q.412, Y.429 Chain B: T.156, T.157, T.158, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.244, N.247, T.275, C.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Ligands: ADN.4 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.223 Hydrogen bonds: B:T.157, B:T.157, B:T.158, B:T.158, B:T.158, B:N.190, B:D.222, B:V.223, B:E.244, B:H.300, B:N.345, B:N.345, A:Q.412, A:Y.429 Water bridges: B:S.186, B:D.222 NAD.5: 28 residues within 4Å: Chain C: T.156, T.157, T.158, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.244, N.247, T.274, T.275, C.277, I.280, I.298, G.299, H.300, L.343, N.345, L.346, H.352 Chain D: L.408, Q.412, Y.429 Ligands: ADN.6 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.223 Hydrogen bonds: C:T.158, C:T.158, C:N.190, C:D.222, C:V.223, C:T.275, C:I.298, C:H.300, C:H.300, C:N.345, D:Q.412, D:Y.429, D:Y.429 NAD.7: 26 residues within 4Å: Chain C: L.408, Q.412, Y.429 Chain D: T.156, T.157, T.158, N.190, G.219, G.221, D.222, V.223, T.241, E.242, I.243, E.244, N.247, T.274, T.275, C.277, I.280, I.298, G.299, H.300, N.345, H.352 Ligands: ADN.8 18 PLIP interactions: 15 interactions with chain D, 3 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:I.243, D:E.244, D:H.300, D:H.300, D:N.345, D:N.345, C:Q.412, C:Y.429, C:Y.429 Water bridges: D:S.186

4 x ADN: ADENOSINE(Non-covalent)

ADN.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: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.58, A:E.58, A:T.156, A:K.185, A:K.185, A:H.300, A:H.352 ADN.4: 19 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.343, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAD.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.56, B:E.58, B:E.58, B:T.156, B:T.156, B:K.185, B:K.185, B:H.300, B:H.352 pi-Stacking: B:H.352 ADN.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: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.58, C:E.155, C:K.185, C:K.185, C:H.300, C:H.352 pi-Stacking: C:H.352 ADN.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: NAD.7 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.56, D:E.58, D:E.155, D:T.156, D:T.156, D:K.185, D:K.185, D:H.300, D:H.352 pi-Stacking: D:H.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komoto, J. et al., Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme. J.Biol.Chem. (2000)

Release Date

2001-01-17

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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