SMTL ID : 6m5o.1

Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

DXC.1: 14 residues within 4Å: Chain A: L.169, L.175, Y.179, I.186, S.229, N.411, A.421, R.428 Chain B: E.101, Y.108, Y.109, F.323, P.324 Ligands: GLY.3 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.108, B:Y.109, B:F.323, B:P.324, A:L.169, A:L.169, A:L.175, A:Y.179 Water bridges: A:S.229, A:T.414 DXC.2: 14 residues within 4Å: Chain A: E.101, Y.108, Y.109, F.323, P.324 Chain B: L.169, L.175, Y.179, I.186, S.229, N.411, K.412, R.428 Ligands: GLY.4 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.108, A:Y.108, A:Y.108, A:Y.109, A:F.323, A:P.324, B:L.169, B:Y.179 Water bridges: B:S.229

2 x GLY: GLYCINE(Non-covalent)

GLY.3: 8 residues within 4Å: Chain A: S.79, H.174, S.229, H.257, K.283, R.428 Chain B: E.101 Ligands: DXC.1 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.79, A:S.229, B:E.101 Water bridges: A:S.229, A:R.428, A:R.428 Salt bridges: A:H.257, A:R.428 GLY.4: 8 residues within 4Å: Chain A: E.101 Chain B: S.79, H.174, S.229, H.257, K.283, R.428 Ligands: DXC.2 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.79, B:S.229, A:E.101 Water bridges: B:S.229 Salt bridges: B:H.257, B:R.428

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, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase, mitochondrial