SMTL ID : 6ti1.1

SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/L-Threonine/Lys230 gem diamine complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 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

2 x 2BO: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine(Covalent)

2BO.2: 18 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: S.55, E.57, Y.65, G.261, G.262 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.203, A:T.227 Hydrogen bonds: A:S.35, A:G.98, A:S.99, A:S.176, A:K.230, B:Y.65, B:G.261, B:G.262 Water bridges: A:S.97, A:S.97, A:N.102, A:H.126, A:S.176, A:H.229, A:R.236 Salt bridges: A:H.204, A:H.229, A:K.230, A:R.363 pi-Stacking: A:H.126 2BO.4: 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 21 PLIP interactions: 4 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:E.57, A:Y.65, B:A.203, B:T.227 Hydrogen bonds: A:G.261, A:G.262, B:G.98, B:S.99, B:S.176, B:S.176, B:K.230 Water bridges: B:S.97, B:S.97, B:N.102, 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 NA: SODIUM ION(Non-functional Binders)

NA.3: 7 residues within 4Å: Chain A: A.203, A.206, T.227, H.229, K.230, T.231, L.232 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.227, A:T.227, A:T.231, A:T.231, A:L.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrillo, G. et al., Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus. To Be Published

Release Date

2020-04-29

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Serine hydroxymethyltransferase

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