SMTL ID : 3ce6.1

Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x ADN: ADENOSINE(Non-covalent)

ADN.1: 19 residues within 4Å: Chain A: L.67, H.68, T.70, Q.72, T.73, D.155, E.217, T.218, K.247, D.251, H.362, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.70, A:Q.72, A:T.73, A:T.218, A:T.218, A:K.247, A:K.247, A:H.362, A:H.415 Water bridges: A:T.413 ADN.3: 19 residues within 4Å: Chain B: L.67, H.68, T.70, Q.72, T.73, D.155, E.217, T.218, K.247, D.251, H.362, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.72, B:T.218, B:K.247, B:K.247, B:H.362, B:H.415 Water bridges: B:Q.72 ADN.5: 19 residues within 4Å: Chain C: L.67, H.68, T.70, Q.72, T.73, D.155, E.217, T.218, K.247, D.251, H.362, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.70, C:Q.72, C:T.73, C:T.218, C:T.218, C:K.247, C:K.247, C:H.362, C:H.415, C:H.415 Water bridges: C:T.413 ADN.7: 19 residues within 4Å: Chain D: L.67, H.68, T.70, Q.72, T.73, D.155, E.217, T.218, K.247, D.251, H.362, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.72, D:T.218, D:K.247, D:K.247, D:H.362, D:H.415 Water bridges: D:Q.72

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

NAD.2: 31 residues within 4Å: Chain A: T.218, T.219, T.220, D.251, N.252, G.281, G.283, D.284, V.285, T.303, E.304, I.305, D.306, N.309, A.336, T.337, G.338, N.339, I.342, I.360, G.361, H.362, L.406, N.408, H.415 Chain B: T.469, L.471, Q.475, K.488, Y.492 Ligands: ADN.1 29 PLIP interactions: 5 interactions with chain B, 24 interactions with chain A Hydrogen bonds: B:Q.475, B:Q.475, B:K.488, B:K.488, B:Y.492, A:T.219, A:T.219, A:T.219, A:T.220, A:T.220, A:N.252, A:D.284, A:V.285, A:T.303, A:I.305, A:D.306, A:N.309, A:N.339, A:H.362, A:N.408, A:N.408 Hydrophobic interactions: A:N.252, A:V.285 Water bridges: A:G.283, A:D.284, A:D.284, A:G.286, A:F.363, A:E.366 NAD.4: 30 residues within 4Å: Chain A: T.469, Q.475, K.488, Y.492 Chain B: T.218, T.219, T.220, D.251, N.252, G.281, G.283, D.284, V.285, T.303, E.304, I.305, D.306, N.309, A.336, T.337, G.338, N.339, I.342, I.360, G.361, H.362, L.406, N.408, H.415 Ligands: ADN.3 28 PLIP interactions: 6 interactions with chain A, 22 interactions with chain B Hydrogen bonds: A:Q.475, A:Q.475, A:K.488, A:K.488, A:Y.492, A:Y.492, B:T.219, B:T.220, B:T.220, B:N.252, B:D.284, B:V.285, B:I.305, B:D.306, B:N.309, B:N.339, B:H.362, B:N.408, B:N.408 Hydrophobic interactions: B:N.252, B:V.285 Water bridges: B:T.219, B:G.283, B:D.284, B:G.286, B:T.303, B:F.363, B:E.366 NAD.6: 30 residues within 4Å: Chain C: T.218, T.219, T.220, D.251, N.252, G.281, G.283, D.284, V.285, T.303, E.304, I.305, D.306, N.309, A.336, T.337, G.338, N.339, I.342, I.360, G.361, H.362, L.406, N.408, H.415 Chain D: T.469, Q.475, K.488, Y.492 Ligands: ADN.5 27 PLIP interactions: 22 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:N.252, C:V.285 Hydrogen bonds: C:T.219, C:T.220, C:T.220, C:T.220, C:N.252, C:D.284, C:V.285, C:T.303, C:I.305, C:D.306, C:N.309, C:N.339, C:H.362, C:N.408, C:N.408, D:Q.475, D:Q.475, D:K.488, D:K.488, D:Y.492 Water bridges: C:G.283, C:D.284, C:D.284, C:G.286, C:F.363 NAD.8: 30 residues within 4Å: Chain C: T.469, Q.475, K.488, Y.492 Chain D: T.218, T.219, T.220, D.251, N.252, G.281, G.283, D.284, V.285, T.303, E.304, I.305, D.306, N.309, A.336, T.337, G.338, N.339, I.342, I.360, G.361, H.362, L.406, N.408, H.415 Ligands: ADN.7 29 PLIP interactions: 22 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:V.285 Hydrogen bonds: D:T.219, D:T.219, D:T.219, D:T.220, D:N.252, D:D.284, D:V.285, D:T.303, D:I.305, D:D.306, D:N.309, D:N.339, D:H.362, D:N.408, D:N.408, C:Q.475, C:Q.475, C:K.488, C:K.488, C:Y.492, C:Y.492 Water bridges: D:T.219, D:G.283, D:D.284, D:G.286, D:F.363, D:E.366, C:T.469

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