SMTL ID : 7r39.2 (1 other biounit)

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Sulfolobus acidocaldarius in complex with adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 29 residues within 4Å: Chain A: T.171, T.172, T.173, D.204, N.205, T.209, I.233, G.234, G.236, W.237, V.238, V.256, E.257, S.258, S.259, R.262, A.289, T.290, G.291, N.292, V.295, S.313, G.314, H.315, N.360, H.367 Chain C: L.423, Q.427 Ligands: ADN.2 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:N.205, A:V.238 Hydrogen bonds: A:T.172, A:T.172, A:T.173, A:T.173, A:N.205, A:W.237, A:V.238, A:S.258, A:S.258, A:S.259, A:R.262, A:T.290, A:N.292, A:H.315, A:N.360, A:N.360, C:Q.427, C:Q.427 Water bridges: A:G.236, A:G.239 Salt bridges: A:R.262 NAD.3: 30 residues within 4Å: Chain B: T.171, T.172, T.173, D.204, N.205, T.209, I.233, G.234, G.236, W.237, V.238, V.256, E.257, S.258, S.259, R.262, A.289, T.290, G.291, N.292, V.295, S.313, G.314, H.315, N.360, L.361, H.367 Chain D: L.423, Q.427 Ligands: ADN.4 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:V.238 Hydrogen bonds: B:T.172, B:T.173, B:T.173, B:N.205, B:W.237, B:V.238, B:S.258, B:S.258, B:S.259, B:R.262, B:R.262, B:T.290, B:N.292, B:H.315, B:N.360, B:N.360, D:Q.427, D:Q.427 Water bridges: B:S.259, B:S.259 Salt bridges: B:R.262 NAD.5: 30 residues within 4Å: Chain A: L.423, Q.427 Chain C: T.171, T.172, T.173, D.204, N.205, T.209, I.233, G.234, G.236, W.237, V.238, V.256, E.257, S.258, S.259, R.262, A.289, T.290, G.291, N.292, V.295, S.313, G.314, H.315, L.358, N.360, H.367 Ligands: ADN.6 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.238 Hydrogen bonds: C:T.172, C:T.173, C:T.173, C:T.173, C:N.205, C:G.236, C:W.237, C:V.238, C:S.258, C:S.258, C:S.259, C:R.262, C:T.290, C:N.292, C:H.315, C:N.360, C:N.360, A:Q.427, A:Q.427 Water bridges: C:G.239 Salt bridges: C:R.262 NAD.7: 28 residues within 4Å: Chain B: Q.427 Chain D: T.171, T.172, T.173, D.204, N.205, T.209, I.233, G.234, G.236, W.237, V.238, V.256, E.257, S.258, S.259, R.262, A.289, T.290, G.291, N.292, V.295, S.313, G.314, H.315, N.360, H.367 Ligands: ADN.8 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:V.238 Hydrogen bonds: D:T.172, D:T.172, D:T.173, D:N.205, D:G.236, D:W.237, D:V.238, D:S.258, D:S.258, D:S.259, D:R.262, D:T.290, D:N.292, D:H.315, D:N.360, D:N.360, B:Q.427, B:Q.427 Water bridges: D:G.239 Salt bridges: D:R.262

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 18 residues within 4Å: Chain A: H.74, T.76, E.78, T.79, D.147, E.170, T.171, K.200, D.204, H.315, L.358, L.361, E.365, G.366, H.367, M.372, F.376 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.76, A:E.78, A:E.170, A:T.171, A:K.200, A:K.200, A:H.315, A:N.360, A:H.367 ADN.4: 18 residues within 4Å: Chain B: H.74, T.76, E.78, T.79, D.147, E.170, T.171, K.200, D.204, H.315, L.358, L.361, E.365, G.366, H.367, M.372, F.376 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.78, B:E.78, B:T.171, B:T.171, B:K.200, B:K.200, B:H.367 ADN.6: 18 residues within 4Å: Chain C: H.74, T.76, E.78, T.79, D.147, E.170, T.171, K.200, D.204, H.315, L.358, L.361, E.365, G.366, H.367, M.372, F.376 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.78, C:T.171, C:T.171, C:K.200, C:D.204, C:H.315, C:H.367 ADN.8: 18 residues within 4Å: Chain D: H.74, T.76, E.78, T.79, D.147, E.170, T.171, K.200, D.204, H.315, L.358, L.361, E.365, G.366, H.367, M.372, F.376 Ligands: NAD.7 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.76, D:E.78, D:E.78, D:T.171, D:T.171, D:K.200, D:K.200, D:H.315, D:H.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saleem-Batcha, R. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from Sulfolobus acidocaldarius in complex with adenosine. To Be Published

Release Date

2023-02-15

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
H

C
D

D
F

Adenosylhomocysteinase

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