SMTL ID : 7o5l.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 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: L.410, Q.414 Ligands: ADN.5 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.159, A:T.159, A:T.159, A:T.160, A:N.192, 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:N.347, C:Q.414 Water bridges: A:T.160, A:N.182, A:G.223, A:G.226, A:T.243, C:Q.414 NAD.7: 30 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 Ligands: ADN.10 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:T.159, B:T.160, B:N.192, B:W.224, B:C.225, B:I.245, B:S.246, B:N.279, B:N.347, B:N.347, D:Q.414 Water bridges: B:T.159, B:T.160, B:N.182, B:G.223, B:W.224, B:G.226, B:T.243, B:S.246, D:Q.414 NAD.12: 30 residues within 4Å: Chain A: L.410, 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.16 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:T.160, C:N.192, 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:E.306, C:N.347, A:Q.414 Water bridges: C:N.182, C:G.223, C:G.226, C:F.303, A:Q.414 NAD.18: 30 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 Ligands: ADN.21 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:T.159, D:T.159, D:T.160, D:T.160, D:N.192, D:W.224, D:C.225, D:I.245, D:S.246, D:N.279, D:N.347, D:N.347, B:Q.414 Water bridges: D:T.159, D:T.160, D:N.182, D:G.223, D:W.224, D:G.226, D:S.246, B:Q.414

10 x RB: RUBIDIUM ION(Non-covalent)

RB.2: 3 residues within 4Å: Chain A: Y.417, S.420, S.423 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.417, A:S.420, H2O.9 RB.3: 3 residues within 4Å: Chain A: K.313, E.314, A.316 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.316 RB.4: 5 residues within 4Å: Chain A: L.85, S.86, T.87, K.107, L.348 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.85 RB.8: 3 residues within 4Å: Chain B: L.348, A.349, A.351 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:L.348, B:A.351, H2O.15, H2O.21 RB.9: 2 residues within 4Å: Chain B: Y.417, S.420 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.417, B:S.420 RB.13: 3 residues within 4Å: Chain C: Y.417, S.420, S.423 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.417, C:S.420, H2O.34 RB.14: 3 residues within 4Å: Chain C: K.313, E.314, A.316 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:A.316 RB.15: 5 residues within 4Å: Chain C: L.85, S.86, T.87, K.107, L.348 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:L.85 RB.19: 3 residues within 4Å: Chain D: L.348, A.349, A.351 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:L.348, D:A.351, H2O.39, H2O.45 RB.20: 2 residues within 4Å: Chain D: Y.417, S.420 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:Y.417, D:S.420

4 x ADN: ADENOSINE(Non-covalent)

ADN.5: 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.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.62, A:E.157, A:T.158, A:T.158, A:K.187, A:K.187, A:H.302, A:H.354 Water bridges: A:T.63 ADN.10: 16 residues within 4Å: Chain B: H.58, T.60, E.62, T.63, D.132, E.157, T.158, K.187, D.191, L.345, E.352, G.353, H.354, M.359, F.363 Ligands: NAD.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.62, B:E.62, B:E.157, B:T.158, B:T.158, B:K.187, B:K.187, B:H.354 Water bridges: B:T.63 ADN.16: 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.12 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.60, C:E.62, C:E.62, C:T.158, C:T.158, C:K.187, C:K.187, C:H.302, C:H.354 ADN.21: 16 residues within 4Å: Chain D: H.58, T.60, E.62, T.63, D.132, E.157, T.158, K.187, D.191, L.345, E.352, G.353, H.354, M.359, F.363 Ligands: NAD.18 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.60, D:E.62, D:T.63, D:T.158, D:T.158, D:K.187, D:K.187, D:H.354

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

CL.6: 1 residues within 4Å: Chain A: R.41 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: R.41 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain C: R.41 Ligand excluded by PLIP CL.22: 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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