SMTL ID : 8jzh.1 (1 other biounit)

C. glutamicum S-adenosylmethionine synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: E.17, A.26, K.76, I.80, A.374, D.375, Y.379 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.76, A:A.374 Water bridges: A:E.17, A:K.76 GOL.2: 5 residues within 4Å: Chain A: R.219, D.224, A.236, I.240, V.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.219, A:R.219, A:D.224, A:A.236 GOL.9: 7 residues within 4Å: Chain B: E.17, A.26, K.76, I.80, A.374, D.375, Y.379 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.76, B:A.374 Water bridges: B:E.17, B:K.76 GOL.10: 5 residues within 4Å: Chain B: R.219, D.224, A.236, I.240, V.242 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.219, B:R.219, B:D.224, B:A.236 GOL.17: 7 residues within 4Å: Chain C: E.17, A.26, K.76, I.80, A.374, D.375, Y.379 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.76, C:A.374 Water bridges: C:E.17, C:K.76 GOL.18: 5 residues within 4Å: Chain C: R.219, D.224, A.236, I.240, V.242 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.219, C:R.219, C:D.224, C:A.236 GOL.25: 7 residues within 4Å: Chain D: E.17, A.26, K.76, I.80, A.374, D.375, Y.379 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.76, D:A.374 Water bridges: D:E.17, D:K.76 GOL.26: 5 residues within 4Å: Chain D: R.219, D.224, A.236, I.240, V.242 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.219, D:R.219, D:D.224, D:A.236

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

PEG.3: 3 residues within 4Å: Chain A: V.7, D.197, T.241 Ligand excluded by PLIP PEG.4: 5 residues within 4Å: Chain A: D.33, A.34, E.37, L.72, P.371 Ligand excluded by PLIP PEG.5: 6 residues within 4Å: Chain A: E.146, E.147, Y.148, K.303, E.392, I.394 Ligand excluded by PLIP PEG.6: 8 residues within 4Å: Chain A: E.147, A.154, H.157, R.158, R.161, Y.379, G.383, R.384 Ligand excluded by PLIP PEG.7: 9 residues within 4Å: Chain A: V.67, E.68, I.69, P.70, V.98 Chain C: V.98, I.100, E.102 Ligands: PEG.23 Ligand excluded by PLIP PEG.11: 3 residues within 4Å: Chain B: V.7, D.197, T.241 Ligand excluded by PLIP PEG.12: 5 residues within 4Å: Chain B: D.33, A.34, E.37, L.72, P.371 Ligand excluded by PLIP PEG.13: 6 residues within 4Å: Chain B: E.146, E.147, Y.148, K.303, E.392, I.394 Ligand excluded by PLIP PEG.14: 8 residues within 4Å: Chain B: E.147, A.154, H.157, R.158, R.161, Y.379, G.383, R.384 Ligand excluded by PLIP PEG.15: 9 residues within 4Å: Chain B: V.67, E.68, I.69, P.70, V.98 Chain D: V.98, I.100, E.102 Ligands: PEG.31 Ligand excluded by PLIP PEG.19: 3 residues within 4Å: Chain C: V.7, D.197, T.241 Ligand excluded by PLIP PEG.20: 5 residues within 4Å: Chain C: D.33, A.34, E.37, L.72, P.371 Ligand excluded by PLIP PEG.21: 6 residues within 4Å: Chain C: E.146, E.147, Y.148, K.303, E.392, I.394 Ligand excluded by PLIP PEG.22: 8 residues within 4Å: Chain C: E.147, A.154, H.157, R.158, R.161, Y.379, G.383, R.384 Ligand excluded by PLIP PEG.23: 9 residues within 4Å: Chain A: V.98, I.100, E.102 Chain C: V.67, E.68, I.69, P.70, V.98 Ligands: PEG.7 Ligand excluded by PLIP PEG.27: 3 residues within 4Å: Chain D: V.7, D.197, T.241 Ligand excluded by PLIP PEG.28: 5 residues within 4Å: Chain D: D.33, A.34, E.37, L.72, P.371 Ligand excluded by PLIP PEG.29: 6 residues within 4Å: Chain D: E.146, E.147, Y.148, K.303, E.392, I.394 Ligand excluded by PLIP PEG.30: 8 residues within 4Å: Chain D: E.147, A.154, H.157, R.158, R.161, Y.379, G.383, R.384 Ligand excluded by PLIP PEG.31: 9 residues within 4Å: Chain B: V.98, I.100, E.102 Chain D: V.67, E.68, I.69, P.70, V.98 Ligands: PEG.15 Ligand excluded by PLIP

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

NA.8: 2 residues within 4Å: Chain A: D.191 Chain D: E.333 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.333 NA.16: 2 residues within 4Å: Chain B: D.191 Chain C: E.333 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.333 NA.24: 2 residues within 4Å: Chain B: E.333 Chain C: D.191 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.191 NA.32: 2 residues within 4Å: Chain A: E.333 Chain D: D.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.333

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
A

C
A

D
A

S-adenosylmethionine synthase

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