SMTL ID : 1k0u.2 (1 other biounit)

Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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, 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: T.406, L.408, Q.412, K.425, Y.429 Ligands: DEA.2 29 PLIP interactions: 22 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:V.223 Hydrogen bonds: A:T.157, A:T.157, A:T.157, A:T.158, A:T.158, A:N.190, A:Y.220, A:D.222, A:V.223, A:G.224, 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:Q.412, B:K.425, B:K.425, B:Y.429, B:Y.429 Water bridges: A:T.158, A:N.180, A:D.222, A:G.276 Salt bridges: B:K.425 NAD.3: 29 residues within 4Å: Chain A: L.408, Q.412, K.425, 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, 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: DEA.4 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:N.190, B:V.223 Hydrogen bonds: 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, A:Q.412, A:K.425, A:K.425, A:Y.429 Water bridges: B:H.161, B:H.300 Salt bridges: A:K.425 NAD.5: 28 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, 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: DEA.6 21 PLIP interactions: 15 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:N.190, C:V.223 Hydrogen bonds: 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:T.275, C:H.300, C:N.345, C:N.345, D:Q.412, D:Q.412, D:K.425, D:K.425, D:Y.429, D:Y.429 Water bridges: C:T.241 NAD.7: 30 residues within 4Å: Chain C: Q.412, K.425, Y.429 Chain D: T.156, T.157, T.158, N.190, C.194, G.219, Y.220, G.221, D.222, V.223, T.241, E.242, I.243, D.244, N.247, T.274, T.275, G.276, I.280, I.298, G.299, H.300, L.343, N.345, L.346, H.352 Ligands: DEA.8 23 PLIP interactions: 18 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:Y.220, D:G.221, 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 DEA: D-ERITADENINE(Non-covalent)

DEA.2: 20 residues within 4Å: Chain A: L.53, H.54, T.56, E.58, T.59, D.130, E.155, T.156, N.180, K.185, D.189, N.190, N.345, L.346, M.350, G.351, H.352, M.357, F.361 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.54, A:E.58, A:T.59, A:D.130, A:T.156, A:H.352, A:H.352, A:H.352 Salt bridges: A:K.185 DEA.4: 17 residues within 4Å: Chain B: L.53, H.54, T.56, E.58, T.59, D.130, E.155, T.156, N.180, K.185, D.189, L.346, M.350, G.351, H.352, M.357 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.54, B:T.56, B:E.58, B:H.352, B:H.352 Water bridges: B:T.156 Salt bridges: B:K.185 DEA.6: 18 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, N.345, 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:H.54, C:T.56, C:E.58, C:N.345, C:H.352, C:H.352 Salt bridges: C:K.185 DEA.8: 18 residues within 4Å: Chain D: L.53, H.54, T.56, E.58, T.59, D.130, E.155, T.156, N.180, K.185, D.189, N.190, L.346, G.351, H.352, M.357, F.361 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.58, D:T.59, D:T.156, D:H.352, D:H.352, D:H.352 Salt bridges: D:K.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y. et al., Inhibition of S-adenosylhomocysteine hydrolase by acyclic sugar adenosine analogue D-eritadenine. Crystal structure of S-adenosylhomocysteine hydrolase complexed with D-eritadenine. J.Biol.Chem. (2002)

Release Date

2001-10-17

Peptides

S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE

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