SMTL ID : 7ll3.1

S-adenosylmethionine synthetase co-crystallized with UppNHp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: E.114, E.307, R.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.114, A:E.307, A:R.337 EDO.2: 4 residues within 4Å: Chain A: T.221, K.222, F.223, F.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.223 Water bridges: A:T.221 EDO.3: 3 residues within 4Å: Chain A: P.213, E.215, W.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.215 EDO.8: 7 residues within 4Å: Chain B: E.130, A.137, P.138, F.171, Y.173, I.178 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain B: E.130, M.255, R.294 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.130, B:R.294, B:R.294 EDO.11: 3 residues within 4Å: Chain C: E.114, E.307, R.337 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.114, C:E.114, C:E.307, C:E.307, C:R.337 EDO.12: 4 residues within 4Å: Chain C: T.221, K.222, F.223, F.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.223 Water bridges: C:T.221 EDO.13: 3 residues within 4Å: Chain C: P.213, E.215, W.216 No protein-ligand interaction detected (PLIP) EDO.18: 7 residues within 4Å: Chain D: E.130, A.137, P.138, F.171, Y.173, I.178 Ligands: EDO.19 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain D: E.130, M.255, R.294 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.130, D:R.294, D:R.294

2 x UNP: 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine(Non-covalent)

UNP.4: 4 residues within 4Å: Chain A: E.307, R.331, D.335, R.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.307, A:D.335 Water bridges: A:E.307, A:F.334 UNP.14: 4 residues within 4Å: Chain C: E.307, R.331, D.335, R.337 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.307, C:D.335 Water bridges: C:E.307, C:F.334

4 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)

PPK.5: 15 residues within 4Å: Chain A: H.15, D.17, K.166, D.239, C.240, R.245, K.246 Chain B: E.43, D.119, G.261, A.262, K.266, D.272 Ligands: MG.6, MG.7 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.17, A:R.245, A:R.245, A:K.246, B:E.43, B:D.119, B:D.119, B:A.262, B:K.266, B:D.272 Water bridges: A:K.166 Salt bridges: A:H.15, A:K.166, A:K.246 PPK.10: 10 residues within 4Å: Chain A: D.119, G.261, A.262, K.266, D.272 Chain B: H.15, D.17, K.166, R.245, K.246 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.17, B:R.245, B:R.245, B:K.246, A:A.262, A:K.266 Salt bridges: B:H.15, B:K.166, B:K.246 PPK.15: 15 residues within 4Å: Chain C: H.15, D.17, K.166, D.239, C.240, R.245, K.246 Chain D: E.43, D.119, G.261, A.262, K.266, D.272 Ligands: MG.16, MG.17 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:E.43, D:E.43, D:D.119, D:D.119, D:A.262, D:K.266, D:D.272, D:D.272, C:R.245, C:R.245, C:K.246 Water bridges: C:K.166 Salt bridges: C:H.15, C:K.166, C:K.246 PPK.20: 10 residues within 4Å: Chain C: D.119, G.261, A.262, K.266, D.272 Chain D: H.15, D.17, K.166, R.245, K.246 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.17, D:D.17, D:R.245, D:R.245, D:K.246, C:A.262, C:K.266 Salt bridges: D:H.15, D:K.166, D:K.246

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: C.240 Chain B: E.43 Ligands: PPK.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.43, H2O.3 MG.7: 4 residues within 4Å: Chain A: E.9, K.246 Chain B: D.272 Ligands: PPK.5 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain C: C.240 Chain D: E.43 Ligands: PPK.15 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.43, H2O.8 MG.17: 4 residues within 4Å: Chain C: E.9, K.246 Chain D: D.272 Ligands: PPK.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gade, M. et al., Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. Jacs Au (2021)

Release Date

2021-03-31

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

S-adenosylmethionine synthase

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