SMTL ID : 6m5w.1

Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 17 residues within 4Å: Chain A: S.139, G.140, S.141, H.168, T.222, S.223, D.248, A.250, H.251, T.274, H.276, K.277 Chain D: Y.93, Y.138, G.322, G.323 Ligands: GLY.12 13 PLIP interactions: 4 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:Y.93, D:Y.138, D:G.322, D:G.323, A:S.139, A:G.140, A:S.141, A:S.141, A:H.251, A:T.274 Hydrophobic interactions: A:H.168 Salt bridges: A:H.276 pi-Stacking: A:H.168 PLP.4: 17 residues within 4Å: Chain B: S.139, G.140, S.141, H.168, T.222, S.223, D.248, A.250, H.251, T.274, H.276, K.277 Chain C: Y.93, Y.138, G.322, G.323 Ligands: GLY.9 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:Y.93, C:Y.138, C:G.322, C:G.323, B:S.139, B:G.140, B:S.141, B:S.141, B:H.251, B:T.274 Hydrophobic interactions: B:H.168 Salt bridges: B:H.276 pi-Stacking: B:H.168 PLP.7: 17 residues within 4Å: Chain B: Y.93, Y.138, G.322, G.323 Chain C: S.139, G.140, S.141, H.168, T.222, S.223, D.248, A.250, H.251, T.274, H.276, K.277 Ligands: GLY.6 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:H.168 Hydrogen bonds: C:S.139, C:G.140, C:S.141, C:S.141, C:H.251, C:T.274, B:Y.93, B:Y.93, B:G.322, B:G.323 Salt bridges: C:H.276 pi-Stacking: C:H.168 PLP.10: 17 residues within 4Å: Chain A: Y.93, Y.138, G.322, G.323 Chain D: S.139, G.140, S.141, H.168, T.222, S.223, D.248, A.250, H.251, T.274, H.276, K.277 Ligands: GLY.3 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:H.168 Hydrogen bonds: D:S.139, D:G.140, D:S.141, D:S.141, D:H.251, D:T.274, A:Y.93, A:Y.93, A:G.322, A:G.323 Salt bridges: D:H.276 pi-Stacking: D:H.168

4 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)

DXC.2: 12 residues within 4Å: Chain A: E.95, Y.102, Y.103, F.317, P.318 Chain D: L.163, F.173, I.180, N.405, N.407, R.422 Ligands: GLY.3 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:Y.102, A:Y.103, A:F.317, A:P.318, D:L.163, D:F.173, D:F.173, D:I.180 Hydrogen bonds: D:R.422, D:R.422 DXC.5: 12 residues within 4Å: Chain B: E.95, Y.102, Y.103, F.317, P.318 Chain C: L.163, F.173, I.180, N.405, N.407, R.422 Ligands: GLY.6 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:Y.102, B:Y.103, B:F.317, B:P.318, C:L.163, C:F.173, C:F.173, C:I.180 Hydrogen bonds: C:R.422, C:R.422 DXC.8: 12 residues within 4Å: Chain B: L.163, F.173, I.180, N.405, N.407, R.422 Chain C: E.95, Y.102, Y.103, F.317, P.318 Ligands: GLY.9 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:Y.102, C:Y.103, C:F.317, C:P.318, B:L.163, B:F.173, B:F.173, B:I.180 Hydrogen bonds: B:R.422, B:R.422 DXC.11: 12 residues within 4Å: Chain A: L.163, F.173, I.180, N.405, N.407, R.422 Chain D: E.95, Y.102, Y.103, F.317, P.318 Ligands: GLY.12 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:Y.102, D:Y.103, D:F.317, D:P.318, A:L.163, A:F.173, A:F.173, A:I.180 Hydrogen bonds: A:R.422, A:R.422

4 x GLY: GLYCINE(Non-covalent)

GLY.3: 10 residues within 4Å: Chain A: E.95, Y.103 Chain D: S.73, H.168, S.223, H.251, K.277, R.422 Ligands: DXC.2, PLP.10 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:Y.103, D:S.73, D:S.73, D:S.223, D:R.422 Salt bridges: D:H.251, D:K.277, D:R.422 GLY.6: 10 residues within 4Å: Chain B: E.95, Y.103 Chain C: S.73, H.168, S.223, H.251, K.277, R.422 Ligands: DXC.5, PLP.7 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.73, C:S.73, C:S.223, C:R.422, B:Y.103 Salt bridges: C:H.251, C:K.277, C:R.422 GLY.9: 10 residues within 4Å: Chain B: S.73, H.168, S.223, H.251, K.277, R.422 Chain C: E.95, Y.103 Ligands: PLP.4, DXC.8 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.73, B:S.73, B:S.223, B:R.422, C:Y.103, C:Y.103 Salt bridges: B:H.251, B:K.277, B:R.422 GLY.12: 10 residues within 4Å: Chain A: S.73, H.168, S.223, H.251, K.277, R.422 Chain D: E.95, Y.103 Ligands: PLP.1, DXC.11 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:Y.103, D:Y.103, A:S.73, A:S.73, A:S.223, A:R.422 Salt bridges: A:H.251, A:K.277, A:R.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ota, T. et al., Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate. Iscience (2021)

Release Date

2021-01-20

Peptides

Serine hydroxymethyltransferase, cytosolic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Serine hydroxymethyltransferase, cytosolic