SMTL ID : 7v3d.1

Complex structure of serine hydroxymethyltransferase from Enterococcus faecium and its inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 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: 13 residues within 4Å: Chain A: L.120, G.124, H.125, L.126, K.345, N.346, S.347, P.355, F.356, R.362 Chain B: E.56, Y.63, Y.64 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: 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:H.125, A:L.126, A:K.345, A:K.345, A:S.347 Water bridges: A:N.346 5M5.4: 15 residues within 4Å: Chain A: E.56, Y.63 Chain B: L.120, G.124, H.125, L.126, V.132, S.175, N.344, K.345, N.346, S.347, P.355, F.356, R.362 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.120, B:L.126, B:V.132, B:P.355, B:F.356, B:F.356, A:Y.63, A:Y.63 Hydrogen bonds: B:G.124, B:H.125, B:L.126, B:K.345, B:S.347 Water bridges: B:N.346, B:N.346

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

PLP.2: 19 residues within 4Å: Chain A: S.96, G.97, S.98, N.101, H.125, T.127, H.128, A.174, S.175, D.200, A.202, H.203, T.226, H.228, K.229 Chain B: Y.54, G.260, G.261 Ligands: CL.3 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.125, A:A.202, A:K.229 Hydrogen bonds: A:G.97, A:S.98, A:N.101, B:G.260, B:G.261 Water bridges: A:S.96, A:S.96, A:T.224 Salt bridges: A:H.228, A:K.229 pi-Stacking: A:H.125 PLP.5: 18 residues within 4Å: Chain A: Y.54, G.260, G.261 Chain B: S.96, G.97, S.98, N.101, H.125, T.127, A.174, S.175, D.200, A.202, H.203, T.226, H.228, K.229 Ligands: CL.6 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:Y.54, A:G.260, A:G.261, B:S.96, B:G.97, B:S.98, B:N.101, B:T.127 Hydrophobic interactions: B:A.202 Water bridges: B:S.96, B:S.96 Salt bridges: B:H.228, B:K.229 pi-Stacking: B:H.125

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: S.34, S.175, H.203, K.229, R.362 Ligands: PLP.2 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: S.175, H.203, K.229, R.362 Ligands: PLP.5 Ligand excluded by PLIP

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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