SMTL ID : 7lnh.1

S-adenosylmethionine synthetase co-crystallized with UppNHp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x YQP: (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-$l^{3}-sulfanyl]butanoic acid(Non-covalent)

YQP.1: 15 residues within 4Å: Chain A: H.29, P.30, D.179, K.181, S.247, R.249, F.250, G.257, D.258 Chain B: A.55, E.70, Q.113, D.116, I.117, K.289 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:D.258, B:I.117 Hydrogen bonds: A:S.247, A:D.258, A:D.258, B:E.70, B:Q.113 Salt bridges: A:D.258, B:K.289 pi-Stacking: A:F.250 YQP.3: 17 residues within 4Å: Chain A: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289 Chain B: H.29, P.30, D.179, K.181, S.247, R.249, F.250, G.257, D.258 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.247, B:D.258, A:E.70, A:Q.113 Salt bridges: B:D.258, A:D.134, A:K.289 pi-Stacking: B:F.250 Water bridges: A:I.117, A:I.117 YQP.4: 15 residues within 4Å: Chain C: H.29, P.30, D.179, K.181, S.247, R.249, F.250, G.257, D.258 Chain D: A.55, E.70, Q.113, D.116, I.117, K.289 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:I.117, C:D.258 Hydrogen bonds: D:E.70, D:E.70, D:Q.113, C:H.29, C:S.247, C:D.258 Salt bridges: D:K.289, C:D.258 pi-Stacking: C:F.250 YQP.6: 17 residues within 4Å: Chain C: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289 Chain D: H.29, P.30, D.179, K.181, S.247, R.249, F.250, G.257, D.258 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:E.70, C:E.70, C:Q.113, D:S.247 Water bridges: C:I.117, C:I.117 Salt bridges: C:D.134, C:K.289, D:D.258 pi-Stacking: D:F.250

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

EDO.2: 1 residues within 4Å: Chain B: Q.112 No protein-ligand interaction detected (PLIP) EDO.5: 1 residues within 4Å: Chain D: Q.112 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

2022-03-02

Peptides

S-adenosylmethionine synthase isoform type-2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

S-adenosylmethionine synthase isoform type-2

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