SMTL ID : 3glq.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei in complex with 9-beta-D-arabino-furansyl-adenine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: T.221, T.222, T.223, D.254, N.255, G.284, G.286, D.287, V.288, T.306, E.307, I.308, D.309, C.312, A.339, T.340, G.341, N.342, I.363, G.364, H.365, L.406, N.408, H.415 Chain B: Q.475, K.488, Y.492 Ligands: RAB.2 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:N.255, A:V.288 Hydrogen bonds: A:T.222, A:T.222, A:T.222, A:T.223, A:N.255, A:D.287, A:V.288, A:I.308, A:D.309, A:N.342, A:H.365, A:N.408, A:N.408, B:Q.475, B:Q.475, B:K.488, B:K.488 Water bridges: A:N.245, A:G.286, A:D.287, A:G.289, A:F.366, A:E.369 NAD.3: 30 residues within 4Å: Chain A: Q.475, K.488, Y.492 Chain B: T.221, T.222, T.223, K.250, D.254, N.255, G.284, G.286, D.287, V.288, T.306, E.307, I.308, D.309, C.312, A.339, T.340, G.341, N.342, V.345, I.363, G.364, H.365, L.406, N.408, H.415 Ligands: RAB.4 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:N.255, B:V.288 Hydrogen bonds: B:T.222, B:T.222, B:T.223, B:T.223, B:N.255, B:G.286, B:D.287, B:V.288, B:I.308, B:D.309, B:N.342, B:H.365, B:N.408, B:N.408, A:Q.475, A:Q.475, A:K.488, A:K.488 Water bridges: B:N.245, B:D.287, B:G.289, B:F.366, B:E.369 NAD.5: 28 residues within 4Å: Chain C: T.221, T.222, T.223, D.254, N.255, G.284, G.286, D.287, V.288, T.306, E.307, I.308, D.309, C.312, A.339, T.340, G.341, N.342, I.363, G.364, H.365, L.406, N.408, H.415 Chain D: Q.475, K.488, Y.492 Ligands: RAB.6 26 PLIP interactions: 21 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:N.255, C:V.288 Hydrogen bonds: C:T.222, C:T.222, C:T.222, C:T.223, C:T.223, C:N.255, C:D.287, C:V.288, C:I.308, C:D.309, C:N.342, C:H.365, C:N.408, C:N.408, D:Q.475, D:Q.475, D:K.488, D:K.488, D:Y.492 Water bridges: C:N.245, C:G.286, C:G.289, C:F.366, C:E.369 NAD.7: 30 residues within 4Å: Chain C: Q.475, K.488, Y.492 Chain D: T.221, T.222, T.223, K.250, D.254, N.255, G.284, G.286, D.287, V.288, T.306, E.307, I.308, D.309, C.312, A.339, T.340, G.341, N.342, V.345, I.363, G.364, H.365, L.406, N.408, H.415 Ligands: RAB.8 24 PLIP interactions: 19 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:N.255, D:V.288 Hydrogen bonds: D:T.222, D:T.222, D:T.223, D:N.255, D:G.286, D:D.287, D:V.288, D:I.308, D:D.309, D:N.342, D:H.365, D:N.408, D:N.408, C:Q.475, C:Q.475, C:K.488, C:K.488, C:Y.492 Water bridges: D:N.245, D:G.289, D:F.366, D:E.369

4 x RAB: 2-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL(Non-covalent)

RAB.2: 19 residues within 4Å: Chain A: L.82, H.83, T.85, Q.87, T.88, D.160, E.220, T.221, K.250, D.254, H.365, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.85, A:Q.87, A:T.88, A:T.221, A:K.250, A:D.254, A:H.365, A:H.415 Water bridges: A:Q.87 RAB.4: 19 residues within 4Å: Chain B: L.82, H.83, T.85, Q.87, T.88, D.160, E.220, T.221, K.250, D.254, H.365, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.87, B:T.88, B:T.221, B:T.221, B:K.250, B:H.365, B:H.415 Water bridges: B:Q.87 RAB.6: 19 residues within 4Å: Chain C: L.82, H.83, T.85, Q.87, T.88, D.160, E.220, T.221, K.250, D.254, H.365, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.87, C:E.220, C:T.221, C:T.221, C:K.250, C:D.254, C:H.365, C:H.415 Water bridges: C:T.413 RAB.8: 19 residues within 4Å: Chain D: L.82, H.83, T.85, Q.87, T.88, D.160, E.220, T.221, K.250, D.254, H.365, L.406, L.409, T.413, G.414, H.415, M.420, F.424 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.85, D:Q.87, D:T.221, D:K.250, D:H.365, D:H.415 Water bridges: D:T.413

Links

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Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei in complex with 9-beta-D-arabino-furansyl-adenine. To be Published

Release Date

2009-03-24

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Adenosylhomocysteinase

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