SMTL ID : 8jzi.1

Mutant S-adenosylmethionine synthase from C. glutamicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Y.140, Y.187, D.191, M.274, R.313, F.335 Chain B: R.276, Y.331 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.140, A:Y.140, A:R.313, B:R.276 Water bridges: A:D.191, A:D.191, A:R.313, B:R.276, B:R.276, B:R.276 GOL.3: 8 residues within 4Å: Chain A: D.133, G.280, A.281, K.285, D.291 Chain B: D.21, R.264, K.265 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.21, B:R.264, B:K.265, A:A.281, A:K.285, A:D.291, A:D.291, A:D.291 Water bridges: B:K.180, B:K.180, A:D.291 GOL.6: 7 residues within 4Å: Chain B: E.17, A.26, K.76, A.374, D.375, A.378, Y.379 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.76, B:A.374 Water bridges: B:E.17, B:K.76, B:A.378 GOL.8: 8 residues within 4Å: Chain A: R.276, Y.331 Chain B: Y.140, Y.187, D.191, M.274, R.313, F.335 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.140, B:Y.140, B:D.191, B:R.313 Water bridges: B:D.191, A:R.276, A:R.276, A:R.276 GOL.9: 8 residues within 4Å: Chain C: Y.140, Y.187, D.191, M.274, R.313, F.335 Chain D: R.276, Y.331 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.140, C:D.191, C:R.313 Water bridges: C:D.191, D:R.276, D:R.276 GOL.12: 4 residues within 4Å: Chain C: L.9 Chain D: P.327, V.328, L.352 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 4 residues within 4Å: Chain A: H.174, V.209, D.210, W.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.210 Water bridges: A:W.213, A:W.213

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

NA.4: 2 residues within 4Å: Chain A: E.333 Chain B: D.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.333 Water bridges: A:F.335 NA.5: 2 residues within 4Å: Chain A: D.191 Chain B: E.333 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.333 NA.10: 2 residues within 4Å: Chain C: D.191 Chain D: E.333 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.333 NA.11: 2 residues within 4Å: Chain C: E.333 Chain D: D.191 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.333

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

EDO.7: 3 residues within 4Å: Chain B: R.162, I.171, H.221 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S. et al., Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum . J.Agric.Food Chem. (2023)

Release Date

2023-10-25

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

S-adenosylmethionine synthase