SMTL ID : 6exi.1

NAD-free crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii complexed with adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-tetramer

Ligands

4 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: ADN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.396 Water bridges: A:Q.94 NA.4: 6 residues within 4Å: Chain B: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.397 Water bridges: B:Q.68 NA.7: 6 residues within 4Å: Chain C: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.68 Water bridges: C:Q.94 NA.11: 6 residues within 4Å: Chain D: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.12 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.398 Water bridges: D:Q.68

8 x ADN: ADENOSINE(Non-covalent)

ADN.2: 16 residues within 4Å: Chain A: L.63, H.64, T.66, Q.68, T.69, D.237, H.348, L.389, N.391, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.66, A:Q.68, A:D.237, A:H.348, A:N.391, A:N.391, A:H.398 ADN.3: 14 residues within 4Å: Chain A: G.267, G.269, S.289, E.290, V.291, D.292, C.295, A.322, T.323, N.325, I.328 Chain B: L.456, Q.460, K.473 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.460, B:K.473, B:K.473, A:V.291, A:D.292, A:N.325 Water bridges: B:Q.460 ADN.5: 16 residues within 4Å: Chain B: L.63, H.64, T.66, Q.68, T.69, K.233, D.237, H.348, N.391, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.68, B:K.233, B:D.237, B:H.348, B:N.391, B:N.391, B:H.398 Water bridges: B:D.237 ADN.6: 14 residues within 4Å: Chain A: L.456, Q.460, K.473 Chain B: G.267, G.269, S.289, E.290, V.291, D.292, C.295, A.322, T.323, N.325, I.328 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.460, A:K.473, A:K.473, B:V.291, B:D.292, B:N.325 Water bridges: A:T.454, A:Q.460 ADN.8: 17 residues within 4Å: Chain C: L.63, H.64, T.66, Q.68, T.69, D.237, N.238, H.348, L.389, N.391, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.68, C:T.69, C:D.237, C:H.348, C:N.391, C:N.391, C:H.398 Water bridges: C:N.238 ADN.9: 13 residues within 4Å: Chain C: G.267, G.269, S.289, E.290, V.291, D.292, C.295, A.322, T.323, N.325, I.328 Chain D: Q.460, K.473 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.473, D:K.473, C:V.291, C:D.292, C:N.325 Water bridges: D:Q.460, D:Q.460 ADN.12: 17 residues within 4Å: Chain D: L.63, H.64, T.66, Q.68, T.69, D.237, N.238, H.348, L.389, N.391, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NA.11 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:T.69, D:T.204, D:N.238, D:H.348, D:N.391, D:N.391, D:H.398 Water bridges: D:K.233, D:N.238 ADN.13: 12 residues within 4Å: Chain C: Q.460, K.473 Chain D: G.267, G.269, S.289, E.290, V.291, D.292, C.295, T.323, N.325, I.328 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:V.291, D:D.292, D:N.325, C:Q.460, C:K.473, C:K.473 Water bridges: C:Q.460

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

PEG.10: 4 residues within 4Å: Chain C: W.363, N.365, D.371, E.386 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.365 Water bridges: C:N.365, C:N.365, C:N.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kailing, L.L. et al., S-Adenosyl-L-Homocysteine Hydrolase Inhibition by a Synthetic Nicotinamide Cofactor Biomimetic. Front Microbiol (2018)

Release Date

2018-09-19

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase

Related Entries With Identical Sequence