SMTL ID : 2zj1.1

Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 3'-keto-aristeromycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-tetramer

Ligands

4 x ARJ: (2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-2-hydroxy-5-(hydroxymethyl)cyclopentanone(Non-covalent)

ARJ.1: 19 residues within 4Å: Chain A: L.68, H.69, T.71, Q.73, T.74, D.156, E.218, T.219, K.248, D.252, H.363, L.407, L.410, T.414, G.415, H.416, M.421, F.425 Ligands: NAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.410 Hydrogen bonds: A:T.71, A:Q.73, A:T.74, A:T.219, A:K.248, A:K.248, A:H.363, A:H.416 Water bridges: A:Q.73 ARJ.3: 19 residues within 4Å: Chain B: L.68, H.69, T.71, Q.73, T.74, D.156, E.218, T.219, K.248, D.252, H.363, L.407, L.410, T.414, G.415, H.416, M.421, F.425 Ligands: NAD.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.410 Hydrogen bonds: B:Q.73, B:K.248, B:K.248, B:H.363, B:H.416 Water bridges: B:Q.73 ARJ.6: 19 residues within 4Å: Chain C: L.68, H.69, T.71, Q.73, T.74, D.156, E.218, T.219, K.248, D.252, H.363, L.407, L.410, T.414, G.415, H.416, M.421, F.425 Ligands: NAD.5 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.410 Hydrogen bonds: C:T.71, C:Q.73, C:T.74, C:T.219, C:K.248, C:K.248, C:H.363, C:H.416 Water bridges: C:T.414 ARJ.7: 19 residues within 4Å: Chain D: L.68, H.69, T.71, Q.73, T.74, D.156, E.218, T.219, K.248, D.252, H.363, L.407, L.410, T.414, G.415, H.416, M.421, F.425 Ligands: NAD.8 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.410 Hydrogen bonds: D:Q.73, D:K.248, D:K.248, D:H.363, D:H.416 Water bridges: D:Q.73

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

NAD.2: 31 residues within 4Å: Chain A: T.219, T.220, T.221, D.252, N.253, G.282, G.284, D.285, V.286, T.304, E.305, I.306, D.307, N.310, A.337, T.338, G.339, N.340, I.343, I.361, G.362, H.363, L.407, N.409, H.416 Chain B: L.472, Q.476, L.480, K.489, Y.493 Ligands: ARJ.1 29 PLIP interactions: 24 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.253, A:V.286 Hydrogen bonds: A:T.220, A:T.220, A:T.220, A:T.221, A:T.221, A:N.253, A:D.285, A:V.286, A:T.304, A:I.306, A:D.307, A:N.310, A:N.340, A:H.363, A:N.409, A:N.409, B:Q.476, B:Q.476, B:K.489, B:K.489, B:Y.493 Water bridges: A:G.284, A:D.285, A:D.285, A:G.287, A:F.364, A:E.367 NAD.4: 30 residues within 4Å: Chain A: Q.476, L.480, K.489, Y.493 Chain B: T.219, T.220, T.221, D.252, N.253, G.282, G.284, D.285, V.286, T.304, E.305, I.306, D.307, N.310, A.337, T.338, G.339, N.340, I.343, I.361, G.362, H.363, L.407, N.409, H.416 Ligands: ARJ.3 29 PLIP interactions: 23 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:N.253, B:V.286 Hydrogen bonds: B:T.220, B:T.220, B:T.220, B:T.221, B:N.253, B:D.285, B:V.286, B:I.306, B:D.307, B:N.310, B:N.340, B:H.363, B:N.409, B:N.409, A:Q.476, A:Q.476, A:K.489, A:K.489, A:Y.493, A:Y.493 Water bridges: B:T.220, B:G.284, B:D.285, B:G.287, B:T.304, B:F.364, B:E.367 NAD.5: 31 residues within 4Å: Chain C: T.219, T.220, T.221, D.252, N.253, G.282, G.284, D.285, V.286, T.304, E.305, I.306, D.307, N.310, A.337, T.338, G.339, N.340, I.343, I.361, G.362, H.363, L.407, N.409, H.416 Chain D: T.470, Q.476, L.480, K.489, Y.493 Ligands: ARJ.6 29 PLIP interactions: 5 interactions with chain D, 24 interactions with chain C Hydrogen bonds: D:Q.476, D:Q.476, D:K.489, D:K.489, D:Y.493, C:T.220, C:T.220, C:T.220, C:T.221, C:T.221, C:N.253, C:D.285, C:V.286, C:T.304, C:I.306, C:D.307, C:N.310, C:N.340, C:H.363, C:N.409, C:N.409 Hydrophobic interactions: C:N.253, C:V.286 Water bridges: C:G.284, C:D.285, C:D.285, C:G.287, C:E.367, C:E.367 NAD.8: 29 residues within 4Å: Chain C: Q.476, K.489, Y.493 Chain D: T.219, T.220, T.221, D.252, N.253, G.282, G.284, D.285, V.286, T.304, E.305, I.306, D.307, N.310, A.337, T.338, G.339, N.340, I.343, I.361, G.362, H.363, L.407, N.409, H.416 Ligands: ARJ.7 29 PLIP interactions: 23 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:N.253, D:V.286 Hydrogen bonds: D:T.220, D:T.220, D:T.221, D:T.221, D:N.253, D:G.284, D:D.285, D:V.286, D:I.306, D:D.307, D:N.310, D:N.340, D:H.363, D:N.409, D:N.409, C:Q.476, C:K.489, C:K.489, C:Y.493, C:Y.493 Water bridges: D:T.220, D:D.285, D:G.287, D:T.304, D:F.364, D:E.367, C:Q.476

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reddy, M.C. et al., Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Protein Sci. (2008)

Release Date

2008-09-16

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

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