SMTL ID : 6tgh.2 (1 other biounit)

SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 7 residues within 4Å: Chain A: A.202, A.205, T.226, H.228, K.229, T.230, L.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.230, A:T.230, A:L.231

1 x EVM: L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene](Non-covalent)

EVM.2: 18 residues within 4Å: Chain A: S.34, S.96, G.97, S.98, H.125, S.175, D.200, A.202, H.203, T.226, H.228, K.229, R.362 Chain B: T.54, E.56, Y.64, G.260, G.261 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:A.202 Hydrogen bonds: A:S.34, A:S.34, A:S.96, A:G.97, A:S.98, A:S.175, A:K.229, B:T.54, B:T.54, B:Y.64, B:G.260, B:G.261 Water bridges: A:S.96, A:N.101, B:E.56, B:G.261 Salt bridges: A:H.203, A:H.228, A:K.229, A:R.362 pi-Stacking: A:H.125

1 x DSN: D-SERINE(Non-covalent)

DSN.3: 9 residues within 4Å: Chain A: E.56, Y.64 Chain B: S.34, H.125, S.175, H.203, K.229, R.362 Ligands: PLP.4 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.34, B:K.229, A:E.56, A:Y.64 Water bridges: B:K.229 Salt bridges: B:H.203, B:K.229, B:R.362

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.4: 15 residues within 4Å: Chain A: G.260, G.261 Chain B: S.96, G.97, S.98, H.125, H.128, S.175, D.200, A.202, H.203, T.226, H.228, K.229 Ligands: DSN.3 15 PLIP interactions: 2 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:G.260, A:G.261, B:G.97, B:S.98, B:N.101 Hydrophobic interactions: B:H.125, B:D.200, B:T.226, B:K.229 Water bridges: B:K.229, B:K.229 Salt bridges: B:H.125, B:H.228, B:R.235 pi-Stacking: B:H.125

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

2020-06-03

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Serine hydroxymethyltransferase

Related Entries With Identical Sequence