SMTL ID : 8cod.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Mus musculus in complex with inosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: T.177, T.178, T.179, N.211, C.215, G.240, Y.241, G.242, D.243, V.244, T.262, E.263, I.264, D.265, N.268, T.295, T.296, G.297, C.298, I.301, I.319, G.320, H.321, L.364, N.366, H.373 Chain C: Q.433, L.437, K.446, Y.450 Ligands: NOS.2 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:V.244 Hydrogen bonds: A:T.178, A:T.179, A:T.179, A:T.179, A:N.211, A:D.243, A:V.244, A:I.264, A:D.265, A:H.321, A:N.366, A:N.366, C:Q.433, C:Q.433, C:K.446, C:K.446, C:Y.450, C:Y.450 Water bridges: A:G.245, A:T.295, C:T.427 NAD.4: 30 residues within 4Å: Chain B: T.177, T.178, T.179, D.210, N.211, C.215, G.240, G.242, D.243, V.244, T.262, E.263, I.264, D.265, N.268, T.295, T.296, G.297, C.298, I.301, I.319, G.320, H.321, L.364, N.366, H.373 Chain D: Q.433, K.446, Y.450 Ligands: NOS.5 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:V.244 Hydrogen bonds: B:T.178, B:T.178, B:T.178, B:T.179, B:N.211, B:G.242, B:D.243, B:V.244, B:I.264, B:D.265, B:H.321, B:N.366, B:H.373, D:Q.433, D:Q.433, D:K.446, D:K.446, D:Y.450 Water bridges: B:G.245, B:T.262, B:F.322, B:E.325 NAD.7: 31 residues within 4Å: Chain A: Q.433, L.437, K.446, Y.450 Chain C: T.177, T.178, T.179, N.211, C.215, G.240, Y.241, G.242, D.243, V.244, T.262, E.263, I.264, D.265, N.268, T.295, T.296, G.297, C.298, I.301, I.319, G.320, H.321, L.364, N.366, H.373 Ligands: NOS.8 22 PLIP interactions: 15 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:V.244 Hydrogen bonds: C:T.178, C:T.179, C:T.179, C:T.179, C:N.211, C:D.243, C:V.244, C:I.264, C:D.265, C:H.321, C:N.366, C:N.366, A:Q.433, A:Q.433, A:K.446, A:K.446, A:Y.450, A:Y.450 Water bridges: C:G.245, C:T.295, A:T.427 NAD.10: 30 residues within 4Å: Chain B: Q.433, K.446, Y.450 Chain D: T.177, T.178, T.179, D.210, N.211, C.215, G.240, G.242, D.243, V.244, T.262, E.263, I.264, D.265, N.268, T.295, T.296, G.297, C.298, I.301, I.319, G.320, H.321, L.364, N.366, H.373 Ligands: NOS.11 23 PLIP interactions: 18 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:V.244 Hydrogen bonds: D:T.178, D:T.178, D:T.178, D:T.179, D:N.211, D:G.242, D:D.243, D:V.244, D:I.264, D:D.265, D:H.321, D:N.366, D:H.373, B:Q.433, B:Q.433, B:K.446, B:K.446, B:Y.450 Water bridges: D:G.245, D:T.262, D:F.322, D:E.325

4 x NOS: INOSINE(Non-covalent)

NOS.2: 19 residues within 4Å: Chain A: L.74, H.75, T.77, E.79, T.80, D.151, E.176, T.177, K.206, D.210, H.321, L.364, L.367, M.371, G.372, H.373, M.378, F.382 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.77, A:E.176, A:T.177, A:T.177, A:K.206, A:H.321, A:H.373 Water bridges: A:D.151 NOS.5: 19 residues within 4Å: Chain B: L.74, H.75, T.77, E.79, T.80, D.151, E.176, T.177, K.206, D.210, H.321, L.364, L.367, M.371, G.372, H.373, M.378, F.382 Ligands: NAD.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.77, B:T.77, B:E.79, B:T.80, B:T.177, B:K.206, B:H.321, B:H.373 NOS.8: 19 residues within 4Å: Chain C: L.74, H.75, T.77, E.79, T.80, D.151, E.176, T.177, K.206, D.210, H.321, L.364, L.367, M.371, G.372, H.373, M.378, F.382 Ligands: NAD.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.77, C:E.176, C:T.177, C:T.177, C:K.206, C:H.321, C:H.373 Water bridges: C:D.151 NOS.11: 19 residues within 4Å: Chain D: L.74, H.75, T.77, E.79, T.80, D.151, E.176, T.177, K.206, D.210, H.321, L.364, L.367, M.371, G.372, H.373, M.378, F.382 Ligands: NAD.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.77, D:T.77, D:E.79, D:T.80, D:T.177, D:K.206, D:H.321, D:H.373

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: E.79, M.371, H.373, P.374 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.371 Water bridges: A:Q.105, A:S.375, B:D.228 NA.6: 4 residues within 4Å: Chain B: E.79, M.371, H.373, P.374 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.79 Water bridges: B:Q.105, B:S.375 NA.9: 4 residues within 4Å: Chain C: E.79, M.371, H.373, P.374 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.79 Water bridges: C:Q.105, C:S.375, D:D.228 NA.12: 4 residues within 4Å: Chain D: E.79, M.371, H.373, P.374 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.79 Water bridges: D:Q.105, D:S.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koeppl, L.H. et al., Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases. Commun Biol (2024)

Release Date

2024-03-06

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Adenosylhomocysteinase