SMTL ID : 6ti4.1

SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/D-Serine/Lys230 gem diamine complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: Y.156, D.183, K.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.183 GOL.3: 3 residues within 4Å: Chain A: R.188, P.219, Y.220 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.188, A:D.192, A:D.192, A:P.219

2 x O3Z: (2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid(Covalent)

O3Z.2: 17 residues within 4Å: Chain A: S.35, S.97, G.98, S.99, H.126, S.176, D.201, A.203, H.204, T.227, H.229, K.230, R.363 Chain B: E.57, Y.65, G.261, G.262 26 PLIP interactions: 21 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.203, A:T.227 Hydrogen bonds: A:S.35, A:S.35, A:G.98, A:S.99, A:H.126, A:S.176, A:K.230, A:K.230, B:E.57, B:Y.65, B:G.261, B:G.262 Water bridges: A:S.97, A:S.97, A:N.102, A:R.236, A:R.236, A:R.236, B:E.57 Salt bridges: A:H.204, A:H.229, A:K.230, A:R.363 pi-Stacking: A:H.126 O3Z.5: 17 residues within 4Å: Chain A: E.57, Y.65, G.261, G.262 Chain B: S.35, S.97, G.98, S.99, H.126, S.176, D.201, A.203, H.204, T.227, H.229, K.230, R.363 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.203, B:T.227 Hydrogen bonds: B:S.35, B:G.98, B:S.99, B:S.99, B:H.204, A:E.57, A:E.57, A:G.261, A:G.262 Water bridges: B:S.97, B:S.97, B:N.102, B:S.176, B:H.229, B:R.236 Salt bridges: B:H.204, B:H.229, B:K.230, B:R.363 pi-Stacking: B:H.126

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: S.55, A.56, E.57, R.63, Y.64, Y.65 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrillo, G. et al., Crystal Structure of Y55S Serine Hydroxymethyltransferase variant from Streptococcus thermophilus in complex with gem-diamine intermediate of D-serine. To Be Published

Release Date

2020-04-15

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Serine hydroxymethyltransferase

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