SMTL ID : 6wkb.1

Human S-adenosylmethionine synthetase co-crystallized with UppNHp and Met

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x U4P: 5'-deoxyuridine(Non-covalent)

U4P.1: 8 residues within 4Å: Chain A: H.29, P.30, D.179, S.247, F.250 Chain B: D.116, I.117 Ligands: MET.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.247 pi-Stacking: A:F.250 Hydrophobic interactions: M.4 U4P.5: 12 residues within 4Å: Chain A: D.116, I.117, D.134 Chain B: H.29, P.30, D.179, K.181, S.247, R.249, F.250, D.258 Ligands: MED.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.247 pi-Stacking: B:F.250

1 x MED: D-METHIONINE(Non-covalent)

MED.2: 10 residues within 4Å: Chain A: A.55, E.70, Q.113, I.117, G.133, D.134, K.289 Chain B: G.257, D.258 Ligands: U4P.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.70, A:Q.113 Salt bridges: A:K.289

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

EDO.3: 1 residues within 4Å: Chain B: Q.112 No protein-ligand interaction detected (PLIP)

1 x MET: METHIONINE(Non-covalent)

MET.4: 9 residues within 4Å: Chain A: K.181, G.257, D.258 Chain B: A.55, E.70, Q.113, I.117, K.289 Ligands: U4P.1 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.117, A:D.258 Hydrogen bonds: B:E.70, B:Q.113, A:D.258, A:D.258 Salt bridges: B:K.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laurino, P. et al., S-adenosylmethionine synthetase. To Be Published

Release Date

2021-04-21

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S-adenosylmethionine synthase isoform type-2

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