SMTL ID : 3one.2 (1 other biounit)

Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with adenine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: T.209, T.210, T.211, D.242, N.243, G.272, G.274, D.275, V.276, T.294, E.295, I.296, D.297, C.300, T.327, T.328, G.329, N.330, I.333, I.351, G.352, H.353, L.398, N.400, H.407 Chain B: L.465, Q.469, K.482, Y.486 Ligands: ADE.3 25 PLIP interactions: 20 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.276 Hydrogen bonds: A:T.210, A:T.211, A:T.211, A:T.211, A:N.243, A:G.274, A:D.275, A:V.276, A:T.294, A:I.296, A:D.297, A:N.330, A:H.353, A:N.400, A:N.400, B:Q.469, B:K.482, B:K.482, B:Y.486 Water bridges: A:N.233, A:G.277, A:F.354, A:E.357, B:Q.469 NAD.5: 30 residues within 4Å: Chain A: L.465, Q.469, K.482, Y.486 Chain B: T.209, T.210, T.211, D.242, N.243, G.272, G.274, D.275, V.276, T.294, E.295, I.296, D.297, C.300, T.327, T.328, G.329, N.330, I.333, I.351, G.352, H.353, L.398, N.400, H.407 Ligands: ADE.8 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.276 Hydrogen bonds: B:T.210, B:T.210, B:T.210, B:T.211, B:N.243, B:G.274, B:D.275, B:V.276, B:I.296, B:D.297, B:N.330, B:H.353, B:N.400, B:N.400, A:Q.469, A:K.482, A:K.482 Water bridges: B:D.275, B:D.275, B:G.277, B:T.294, B:F.354, B:E.357, A:Q.469

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 6 residues within 4Å: Chain A: L.462, T.463, K.464, V.477, E.478, Y.481 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.478, A:Y.481 Water bridges: A:E.478, A:E.478 TRS.6: 6 residues within 4Å: Chain B: L.462, T.463, K.464, V.477, E.478, Y.481 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.478, B:Y.481, B:Y.481 TRS.7: 5 residues within 4Å: Chain B: E.364, V.369, K.370, R.371, W.381 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.371, B:R.371 Water bridges: B:E.364, B:R.371

2 x ADE: ADENINE(Non-covalent)

ADE.3: 11 residues within 4Å: Chain A: H.65, T.67, Q.69, T.70, L.401, T.405, G.406, H.407, M.412, F.416 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.69, A:T.70, A:H.407 Water bridges: A:H.65, A:H.65 ADE.8: 11 residues within 4Å: Chain B: H.65, T.67, Q.69, T.70, L.401, T.405, G.406, H.407, M.412, F.416 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.67, B:Q.69, B:H.407 Water bridges: B:H.65, B:H.65, B:D.242, B:D.242

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

NA.4: 5 residues within 4Å: Chain A: Q.69, T.405, G.406, H.407, P.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.405 NA.9: 5 residues within 4Å: Chain B: Q.69, T.405, G.406, H.407, P.408 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.405, B:T.405

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brzezinski, K. et al., High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). Acta Crystallogr.,Sect.D (2012)

Release Date

2011-08-31

Peptides

Adenosylhomocysteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosylhomocysteinase

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