SMTL ID : 7o5m.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Na+ cations

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 6 residues within 4Å: Chain A: I.51, N.127, S.149, D.150, I.152, K.377 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.377 1PE.7: 6 residues within 4Å: Chain C: I.51, N.127, S.149, D.150, I.152, K.377 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.377

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

NAD.2: 29 residues within 4Å: Chain A: T.158, T.159, T.160, D.191, N.192, T.196, G.221, Y.222, G.223, W.224, C.225, T.243, E.244, I.245, S.246, P.249, V.276, T.277, G.278, N.279, V.282, S.300, G.301, H.302, L.345, N.347, H.354 Chain C: Q.414 Ligands: ADN.3 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.159, A:T.159, A:T.159, A:T.160, A:T.160, A:N.192, A:Y.222, A:W.224, A:C.225, A:I.245, A:S.246, A:N.279, A:S.300, A:H.302, A:E.306, A:E.306, A:N.347, C:Q.414 Water bridges: A:N.182, A:G.223, A:W.224, A:F.303, C:Q.414 NAD.5: 29 residues within 4Å: Chain B: T.158, T.159, T.160, D.191, N.192, T.196, G.221, Y.222, G.223, W.224, C.225, T.243, E.244, I.245, S.246, P.249, V.276, T.277, G.278, N.279, V.282, S.300, G.301, H.302, L.345, N.347, H.354 Chain D: L.410, Q.414 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:T.159, B:T.159, B:T.160, B:T.160, B:N.192, B:W.224, B:C.225, B:I.245, B:S.246, B:N.279, B:H.302, B:N.347, B:N.347, D:Q.414 Water bridges: B:T.160, B:N.182, B:G.223, B:W.224, B:G.226, B:S.246, B:F.303, D:D.408, D:Q.414 NAD.8: 29 residues within 4Å: Chain A: Q.414 Chain C: T.158, T.159, T.160, D.191, N.192, T.196, G.221, Y.222, G.223, W.224, C.225, T.243, E.244, I.245, S.246, P.249, V.276, T.277, G.278, N.279, V.282, S.300, G.301, H.302, L.345, N.347, H.354 Ligands: ADN.9 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.159, C:T.159, C:T.159, C:T.160, C:N.192, C:Y.222, C:W.224, C:C.225, C:I.245, C:S.246, C:N.279, C:S.300, C:H.302, C:E.306, C:N.347, A:Q.414 Water bridges: C:N.182, C:G.223, C:W.224, C:T.243, C:F.303, A:Q.414 NAD.11: 29 residues within 4Å: Chain B: L.410, Q.414 Chain D: T.158, T.159, T.160, D.191, N.192, T.196, G.221, Y.222, G.223, W.224, C.225, T.243, E.244, I.245, S.246, P.249, V.276, T.277, G.278, N.279, V.282, S.300, G.301, H.302, L.345, N.347, H.354 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:T.159, D:T.160, D:N.192, D:W.224, D:C.225, D:I.245, D:S.246, D:N.279, D:H.302, D:N.347, D:N.347, B:Q.414 Water bridges: D:T.160, D:N.182, D:G.223, D:W.224, D:G.226, D:T.243, D:S.246, D:F.303, B:Q.414

2 x ADN: ADENOSINE(Non-covalent)

ADN.3: 18 residues within 4Å: Chain A: H.58, T.60, E.62, T.63, D.132, E.157, T.158, K.187, D.191, H.302, L.345, L.348, E.352, G.353, H.354, M.359, F.363 Ligands: NAD.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.60, A:E.62, A:E.62, A:T.63, A:T.158, A:T.158, A:K.187, A:K.187, A:H.302, A:H.354 Water bridges: A:H.58, A:T.61 ADN.9: 18 residues within 4Å: Chain C: H.58, T.60, E.62, T.63, D.132, E.157, T.158, K.187, D.191, H.302, L.345, L.348, E.352, G.353, H.354, M.359, F.363 Ligands: NAD.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.62, C:E.157, C:T.158, C:T.158, C:K.187, C:K.187, C:H.302, C:H.354 Water bridges: C:H.58, C:T.61

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: R.41 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain B: R.41 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain C: R.41 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain D: R.41 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-04-20

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

Adenosylhomocysteinase

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