SMTL ID : 5m67.1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenine and 2'-deoxyadenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: Q.68, M.396, G.397, H.398, P.399 Ligands: ADE.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.68 Water bridges: A:Q.68 NA.2: 0 residues within 4Å: (No contacts) 7 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D, 2 interactions with chain A Water bridges: C:Q.281, C:Q.281, C:Q.281, D:Q.281, D:Q.281, A:Q.281, A:Q.281 NA.6: 6 residues within 4Å: Chain B: Q.68, M.396, G.397, H.398, P.399 Ligands: ADE.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.396 Water bridges: B:Q.68 NA.11: 6 residues within 4Å: Chain C: Q.68, M.396, G.397, H.398, P.399 Ligands: 3D1.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.396 Water bridges: C:Q.94 NA.15: 6 residues within 4Å: Chain D: Q.68, M.396, G.397, H.398, P.399 Ligands: 3D1.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.68 Water bridges: D:Q.94

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

NAD.3: 30 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, K.473, Y.477 Ligands: ADE.4 27 PLIP interactions: 21 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:N.238, A:V.271 Hydrogen bonds: A:T.205, A:T.205, A:T.205, 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:H.348, A:N.391, A:N.391, B:Q.460, B:K.473, B:K.473, B:Y.477, B:Y.477 Water bridges: A:N.228, A:D.270, A:G.272, A:F.349, A:E.352, B:Q.460 NAD.7: 31 residues within 4Å: Chain A: L.456, Q.460, K.473, Y.477 Chain B: T.204, T.205, T.206, D.237, N.238, C.242, 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: ADE.8 28 PLIP interactions: 23 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.205, 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:I.346, B:H.348, B:N.391, A:Q.460, A:Q.460, A:K.473, A:K.473 Water bridges: B:N.228, B:D.270, B:G.272, B:S.289, B:F.349, B:E.352, A:R.457 NAD.12: 31 residues within 4Å: Chain C: T.204, T.205, T.206, D.237, N.238, C.242, 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: 3D1.13 25 PLIP interactions: 20 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:V.271 Hydrogen bonds: C:T.205, C:T.205, C:T.205, C:T.206, C:N.238, C:G.269, C:D.270, C:V.271, C:V.291, C:D.292, C:N.325, C:H.348, C:N.391, C:N.391, D:Q.460, D:Q.460, D:K.473, D:K.473, D:Y.477 Water bridges: C:N.228, C:G.272, C:S.289, C:F.349, C:E.352 NAD.16: 31 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, C.242, 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: 3D1.17 27 PLIP interactions: 22 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:N.238, D:V.271 Hydrogen bonds: D:T.205, D:T.205, D:T.205, 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:H.348, D:N.391, D:N.391, C:Q.460, C:K.473, C:K.473, C:Y.477 Water bridges: D:N.228, D:G.272, D:S.289, D:G.324, D:F.349, C:Q.460

2 x ADE: ADENINE(Non-covalent)

ADE.4: 13 residues within 4Å: Chain A: L.63, H.64, T.66, Q.68, T.69, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.1, NAD.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.68, A:T.69, A:H.398 Water bridges: A:D.141, A:E.203, A:D.237, A:D.237, A:D.237, A:H.398 ADE.8: 13 residues within 4Å: Chain B: L.63, H.64, T.66, Q.68, T.69, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.6, NAD.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.398 Water bridges: B:D.141, B:D.237, B:D.237, B:H.398

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

PEG.5: 7 residues within 4Å: Chain A: R.243, E.244, Q.281 Chain C: R.251, Q.281, A.282, G.283 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Water bridges: B:E.302, A:R.243 Hydrogen bonds: A:R.243, C:R.251 PEG.9: 6 residues within 4Å: Chain B: D.25, F.26, K.29 Chain D: I.366, K.367, P.368 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.25 PEG.18: 7 residues within 4Å: Chain B: R.251, Q.281, A.282, G.283 Chain D: R.243, E.244, Q.281 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:R.243, B:R.251 Water bridges: D:R.243, D:V.247, C:E.302

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 5 residues within 4Å: Chain B: D.350, I.355, A.356, R.359, R.388 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.355 Salt bridges: B:R.359, B:R.388 ACT.14: 4 residues within 4Å: Chain C: D.350, I.355, A.356, R.359 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.355 Water bridges: C:E.169 Salt bridges: C:R.359

2 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)

3D1.13: 20 residues within 4Å: Chain C: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, H.348, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.11, NAD.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.68, C:T.204, C:K.233, C:H.348, C:H.398 3D1.17: 19 residues within 4Å: Chain D: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, H.348, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.15, NAD.16 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.204, D:T.204, D:K.233, D:H.348, D:H.398 Water bridges: D:D.141

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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