SMTL ID : 3ond.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: T.209, T.210, T.211, D.242, N.243, C.247, 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: ADN.3 24 PLIP interactions: 5 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:Q.469, B:K.482, B:K.482, B:Y.486, A:T.210, A:T.210, A:T.210, 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:N.400, A:N.400 Water bridges: B:Q.469, A:N.233, A:G.277 Hydrophobic interactions: A:N.243, A:V.276 NAD.5: 31 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, C.247, 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: ADN.8 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:N.243, 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:N.400, B:N.400, A:Q.469, A:K.482, A:K.482 Water bridges: B:T.211, B:T.211, B:D.275, B:D.275, B:G.277, B:T.294, A:Q.469 NAD.10: 31 residues within 4Å: Chain C: T.209, T.210, T.211, D.242, N.243, C.247, 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 D: L.465, Q.469, K.482, Y.486 Ligands: ADN.12 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:N.243, C:V.276 Hydrogen bonds: C:T.210, C:T.210, C:T.210, C:T.211, C:N.243, C:G.274, C:D.275, C:V.276, C:I.296, C:D.297, C:N.330, C:N.400, C:N.400, D:Q.469, D:K.482, D:K.482 Water bridges: C:T.211, C:T.211, C:D.275, C:D.275, C:G.277, C:T.294, D:Q.469 NAD.14: 31 residues within 4Å: Chain C: L.465, Q.469, K.482, Y.486 Chain D: T.209, T.210, T.211, D.242, N.243, C.247, 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: ADN.17 24 PLIP interactions: 5 interactions with chain C, 19 interactions with chain D Hydrogen bonds: C:Q.469, C:K.482, C:K.482, C:Y.486, D:T.210, D:T.210, D:T.210, D:T.211, D:T.211, D:N.243, D:G.274, D:D.275, D:V.276, D:T.294, D:I.296, D:D.297, D:N.330, D:N.400, D:N.400 Water bridges: C:Q.469, D:N.233, D:G.277 Hydrophobic interactions: D:N.243, D:V.276

6 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.478, A:Y.481 TRS.6: 6 residues within 4Å: Chain B: L.462, T.463, K.464, V.477, E.478, Y.481 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.481, B:Y.481 Water bridges: B:E.478, B:E.478, B:E.478 TRS.7: 5 residues within 4Å: Chain B: E.364, V.369, K.370, R.371, W.381 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.364, B:E.364, B:V.369, B:R.371 Water bridges: B:E.364, B:R.371 TRS.11: 6 residues within 4Å: Chain C: L.462, T.463, K.464, V.477, E.478, Y.481 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.478, C:Y.481, C:Y.481 TRS.15: 6 residues within 4Å: Chain D: L.462, T.463, K.464, V.477, E.478, Y.481 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.481 Water bridges: D:E.478, D:E.478, D:E.478 TRS.16: 5 residues within 4Å: Chain D: E.364, V.369, K.370, R.371, W.381 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.364, D:E.364, D:V.369, D:R.371 Water bridges: D:E.364, D:E.364, D:R.371

4 x ADN: ADENOSINE(Non-covalent)

ADN.3: 17 residues within 4Å: Chain A: H.65, T.67, Q.69, T.70, D.142, E.208, T.209, K.238, D.242, L.398, L.401, T.405, G.406, H.407, M.412, F.416 Ligands: NAD.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.69, A:T.70, A:E.208, A:T.209, A:T.209, A:K.238, A:K.238, A:H.407 Water bridges: A:H.65, A:D.142, A:D.142, A:D.142 ADN.8: 17 residues within 4Å: Chain B: H.65, T.67, Q.69, T.70, D.142, E.208, T.209, K.238, D.242, L.398, L.401, T.405, G.406, H.407, M.412, F.416 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.67, B:Q.69, B:T.209, B:K.238, B:K.238, B:H.407 Water bridges: B:H.65, B:D.142, B:D.142 ADN.12: 17 residues within 4Å: Chain C: H.65, T.67, Q.69, T.70, D.142, E.208, T.209, K.238, D.242, L.398, L.401, T.405, G.406, H.407, M.412, F.416 Ligands: NAD.10 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.67, C:Q.69, C:T.209, C:K.238, C:K.238, C:H.407 Water bridges: C:H.65, C:D.142, C:D.142, C:D.142, C:D.142 ADN.17: 17 residues within 4Å: Chain D: H.65, T.67, Q.69, T.70, D.142, E.208, T.209, K.238, D.242, L.398, L.401, T.405, G.406, H.407, M.412, F.416 Ligands: NAD.14 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.69, D:T.70, D:E.208, D:T.209, D:T.209, D:K.238, D:K.238, D:H.407 Water bridges: D:H.65, D:D.142, D:D.142, D:D.142

4 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:H.407 NA.13: 5 residues within 4Å: Chain C: Q.69, T.405, G.406, H.407, P.408 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.405, C:T.405 NA.18: 5 residues within 4Å: Chain D: Q.69, T.405, G.406, H.407, P.408 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.407

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Adenosylhomocysteinase

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