SMTL ID : 5m65.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 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.2 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.271 Hydrogen bonds: A:T.205, A:T.206, A:T.206, A:N.238, 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:G.269, A:G.272, B:Q.460 NAD.7: 30 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, 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 26 PLIP interactions: 5 interactions with chain A, 21 interactions with chain B Hydrogen bonds: A:K.473, A:K.473, A:Y.477, 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:H.348, B:N.391, B:N.391 Water bridges: A:Q.460, A:Q.460, B:D.270, B:D.270, B:G.272, B:G.324, B:F.349 Hydrophobic interactions: B:V.271

2 x ADE: ADENINE(Non-covalent)

ADE.2: 11 residues within 4Å: Chain A: H.64, T.66, Q.68, T.69, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.68, A:H.398 Water bridges: A:H.64, A:D.141 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: NAD.7, NA.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.398 Water bridges: B:H.64, B:D.141, B:D.237

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

NA.3: 4 residues within 4Å: Chain A: Q.68, M.396, G.397, H.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.68 Water bridges: A:Q.94 NA.9: 5 residues within 4Å: Chain B: Q.68, M.396, G.397, H.398 Ligands: ADE.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68 Water bridges: B:Q.68

2 x BR: BROMIDE ION(Non-covalent)

BR.4: 1 residues within 4Å: Chain A: D.377 Ligand excluded by PLIP BR.10: 1 residues within 4Å: Chain B: D.377 Ligand excluded by PLIP

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: E.37, F.401, K.448, I.449 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.448 Water bridges: A:K.448 EDO.6: 4 residues within 4Å: Chain A: S.474, H.476, Y.477 Chain B: D.229 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.229, A:S.474, A:S.474 Water bridges: A:S.474 EDO.11: 4 residues within 4Å: Chain B: T.205, T.206, H.209, G.324 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: F.401, K.448, I.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.448 Water bridges: B:K.448 EDO.13: 2 residues within 4Å: Chain B: F.26, K.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.29 Water bridges: B:F.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manszewski, T. et al., Crystallographic and SAXS studies ofS-adenosyl-l-homocysteine hydrolase fromBradyrhizobium elkanii. IUCrJ (2017)

Release Date

2017-05-10

Peptides

Adenosylhomocysteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosylhomocysteinase

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