SMTL ID : 7x5n.1

Crystal structure of E. faecium SHMT in complex with (+)-SHIN-1 and PLP-Ser

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 5M5: (4R)-6-azanyl-4-[3-(hydroxymethyl)-5-phenyl-phenyl]-3-methyl-4-propan-2-yl-1H-pyrano[2,3-c]pyrazole-5-carbonitrile(Non-covalent)

5M5.1: 15 residues within 4Å: Chain A: L.120, G.124, H.125, L.126, S.175, K.345, N.346, S.347, P.355, F.356, R.362 Chain B: E.56, Y.63, Y.64 Ligands: PLS.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.120, A:L.126, A:L.126, A:P.355, A:F.356, B:Y.63, B:Y.63, B:Y.64 Hydrogen bonds: A:G.124, A:L.126, A:S.175, A:K.345, A:S.347 Water bridges: A:N.346, A:N.346 5M5.3: 16 residues within 4Å: Chain A: E.56, Y.63, Y.64 Chain B: L.120, G.124, H.125, L.126, V.132, S.175, K.345, N.346, S.347, P.355, F.356, R.362 Ligands: PLS.4 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:Y.63, A:Y.63, B:L.120, B:L.126, B:L.126, B:V.132, B:F.356, B:F.356 Hydrogen bonds: B:L.126, B:S.175, B:K.345, B:S.347 Water bridges: B:G.123, B:N.346

2 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)

PLS.2: 20 residues within 4Å: Chain A: S.34, S.96, G.97, S.98, N.101, H.125, A.174, S.175, D.200, A.202, H.203, T.226, H.228, K.229, R.362 Chain B: Y.54, E.56, G.260, G.261 Ligands: 5M5.1 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.202 Hydrogen bonds: A:S.34, A:S.96, A:G.97, A:S.98, A:N.101, A:S.175, A:S.175, A:K.229, B:Y.54, B:E.56, B:G.260, B:G.261 Water bridges: A:S.96, A:S.96, A:T.224 Salt bridges: A:H.203, A:H.228, A:K.229, A:R.362 pi-Stacking: A:H.125 PLS.4: 21 residues within 4Å: Chain A: Y.54, E.56, Y.64, G.260, G.261 Chain B: S.34, S.96, G.97, S.98, N.101, H.125, A.174, S.175, D.200, A.202, H.203, T.226, H.228, K.229, R.362 Ligands: 5M5.3 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.202 Hydrogen bonds: B:S.34, B:G.97, B:S.98, B:N.101, B:S.175, B:S.175, B:K.229, A:Y.54, A:E.56, A:Y.64, A:G.260, A:G.261 Water bridges: B:S.96, B:S.96, B:R.235 Salt bridges: B:H.203, B:H.228, B:K.229, B:R.362 pi-Stacking: B:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makino, Y. et al., Serine hydroxymethyltransferase as a potential target of antibacterial agents acting synergistically with one-carbon metabolism-related inhibitors. Commun Biol (2022)

Release Date

2022-07-06

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase

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