SMTL ID : 5m66.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 32 residues within 4Å: Chain A: T.204, T.205, T.206, D.237, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398 Chain B: L.456, Q.460, I.464, K.473, Y.477 Ligands: ADN.2, PEG.9 24 PLIP interactions: 5 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:Q.460, B:K.473, B:K.473, B:Y.477, A:T.205, A:T.206, A:T.206, A:N.238, A:G.269, A:D.270, A:V.271, A:V.291, A:D.292, A:N.325, A:N.391, A:N.391 Water bridges: B:Q.460, A:T.206, A:N.228, A:D.270, A:G.272, A:S.289 Hydrophobic interactions: A:N.238, A:V.271 NAD.5: 31 residues within 4Å: Chain A: L.456, Q.460, K.473, Y.477 Chain B: T.204, T.205, T.206, K.233, D.237, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398 Ligands: ADN.6 25 PLIP interactions: 20 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:N.238, B:V.271 Hydrogen bonds: B:T.205, B:T.205, B:T.206, B:T.206, B:T.206, B:N.238, B:G.269, B:D.270, B:V.271, B:V.291, B:D.292, B:N.325, B:N.391, B:N.391, A:Q.460, A:Q.460, A:K.473, A:K.473, A:Y.477 Water bridges: B:D.270, B:D.270, B:G.272, B:S.289 NAD.10: 30 residues within 4Å: Chain C: T.204, T.205, T.206, D.237, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398 Chain D: L.456, Q.460, K.473, Y.477 Ligands: ADN.11 23 PLIP interactions: 18 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:N.238, C:V.271 Hydrogen bonds: C:T.205, C:T.205, C:T.206, C:T.206, C:N.238, C:D.270, C:V.271, C:V.291, C:D.292, C:N.325, C:I.346, C:N.391, D:Q.460, D:K.473, D:K.473, D:Y.477 Water bridges: C:N.228, C:G.269, C:G.272, C:S.289, D:Q.460 NAD.15: 30 residues within 4Å: Chain C: L.456, Q.460, K.473, Y.477 Chain D: T.204, T.205, T.206, D.237, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398 Ligands: ADN.16 25 PLIP interactions: 19 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:N.238, D:V.271 Hydrogen bonds: D:T.205, D:T.205, D:T.206, D:T.206, D:T.206, D:N.238, D:G.269, D:D.270, D:V.271, D:V.291, D:D.292, D:N.325, D:N.391, D:N.391, C:Q.460, C:K.473, C:K.473, C:Y.477, C:Y.477 Water bridges: D:N.228, D:G.272, D:S.289, C:Q.460

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 19 residues within 4Å: Chain A: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.1, NA.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.68, A:T.69, A:T.204, A:K.233, A:K.233, A:H.398 ADN.6: 19 residues within 4Å: Chain B: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.5, NA.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:T.204, B:T.204, B:K.233, B:K.233, B:H.398 ADN.11: 18 residues within 4Å: Chain C: H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.10, NA.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.64, C:Q.68, C:E.203, C:T.204, C:K.233, C:K.233, C:H.398 Water bridges: C:D.141 ADN.16: 18 residues within 4Å: Chain D: H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.15, NA.17 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:E.203, D:T.204, D:T.204, D:K.233, D:K.233, D:H.398, D:H.398 Water bridges: D:D.141

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

NA.3: 6 residues within 4Å: Chain A: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.396 Water bridges: A:Q.68 NA.7: 6 residues within 4Å: Chain B: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.68 NA.12: 6 residues within 4Å: Chain C: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.68 Water bridges: C:Q.94 NA.17: 6 residues within 4Å: Chain D: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.68, D:H.398

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: E.416, N.420, Y.426, P.434, T.436 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.420, A:Y.426, A:T.436 PEG.8: 6 residues within 4Å: Chain A: H.209 Chain B: I.464, G.465, V.466, K.473, S.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.209 PEG.9: 8 residues within 4Å: Chain A: T.205, H.209, Y.212, D.229 Chain B: S.474, H.476, Y.477 Ligands: NAD.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.209, A:Y.212, A:Y.212, B:S.474 Water bridges: A:N.228 PEG.13: 5 residues within 4Å: Chain C: G.465, V.466, P.471, K.473, S.474 No protein-ligand interaction detected (PLIP) PEG.14: 5 residues within 4Å: Chain C: M.147, E.171, F.174, R.210, F.349 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manszewski, T. et al., Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii. IUCrJ (2017)

Release Date

2017-05-10

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

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