SMTL ID : 8gkz.1

Human mitochondrial serine hydroxymethyltransferase (SHMT2) Y105F in complex with PLP, glycine and AGF362 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x GLY: GLYCINE(Non-covalent)

GLY.1: 9 residues within 4Å: Chain A: S.65, H.160, S.215, H.243, R.414 Chain B: E.87, Y.95 Ligands: PLP.2, Y72.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.65, A:H.160, B:E.87, B:Y.95 Salt bridges: A:H.243, A:K.269, A:R.414 GLY.4: 10 residues within 4Å: Chain A: Y.85, E.87, Y.95 Chain B: S.65, H.160, S.215, H.243, K.269, R.414 Ligands: PLP.5 7 PLIP interactions: 5 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.65, B:S.215, G.4, G.4 Salt bridges: B:H.243, B:K.269, B:R.414 GLY.6: 9 residues within 4Å: Chain C: S.65, H.160, S.215, H.243, R.414 Chain D: E.87, Y.95 Ligands: PLP.7, Y72.8 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.65, C:H.160, D:E.87, D:Y.95 Salt bridges: C:H.243, C:K.269, C:R.414 GLY.9: 10 residues within 4Å: Chain C: Y.85, E.87, Y.95 Chain D: S.65, H.160, S.215, H.243, K.269, R.414 Ligands: PLP.10 9 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:S.65, D:S.215, D:K.269, C:Y.95, G.9, G.9 Salt bridges: D:H.243, D:K.269, D:R.414

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

PLP.2: 18 residues within 4Å: Chain A: S.131, G.132, S.133, N.136, H.160, T.162, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269 Chain B: Y.85, G.314, G.315 Ligands: GLY.1 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:K.269 Hydrogen bonds: A:G.132, A:S.133, A:N.136, A:K.269, B:Y.85, B:Y.130, B:G.314, B:G.315 Salt bridges: A:H.268, A:K.269 pi-Stacking: A:H.160 PLP.5: 17 residues within 4Å: Chain A: Y.85, G.314, G.315 Chain B: S.131, G.132, S.133, N.136, H.160, T.162, T.214, S.215, D.240, A.242, H.243, H.268, K.269 Ligands: GLY.4 15 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:K.269 Hydrogen bonds: B:G.132, B:S.133, B:N.136, B:T.266, B:T.266, B:K.269, A:Y.85, A:Y.130, A:G.314, A:G.315, G.4 Salt bridges: B:H.268, B:K.269 pi-Stacking: B:H.160 PLP.7: 18 residues within 4Å: Chain C: S.131, G.132, S.133, N.136, H.160, T.162, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269 Chain D: Y.85, G.314, G.315 Ligands: GLY.6 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:G.314, D:G.315, C:G.132, C:S.133, C:N.136 Hydrophobic interactions: C:K.269 Water bridges: C:T.264 Salt bridges: C:H.268, C:K.269 pi-Stacking: C:H.160 PLP.10: 17 residues within 4Å: Chain C: Y.85, G.314, G.315 Chain D: S.131, G.132, S.133, N.136, H.160, T.162, T.214, S.215, D.240, A.242, H.243, H.268, K.269 Ligands: GLY.9 13 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: D:K.269 Hydrogen bonds: D:G.132, D:S.133, D:N.136, D:T.162, D:T.266, D:T.266, C:G.314, C:G.315, G.9 Salt bridges: D:H.268, D:K.269 pi-Stacking: D:H.160

2 x Y72: N-{4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-3-fluorothiophene-2-carbonyl}-L-glutamic acid(Non-covalent)

Y72.3: 15 residues within 4Å: Chain A: L.155, G.158, G.159, H.160, L.161, S.215, A.216, N.397 Chain B: E.87, F.94, Y.95, F.306, F.309, P.310 Ligands: GLY.1 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.155, A:L.161, B:F.94, B:F.94, B:Y.95, B:F.306, B:F.306, B:F.309 Hydrogen bonds: A:G.159, A:G.159, A:L.161, A:S.215, A:A.216 Y72.8: 15 residues within 4Å: Chain C: L.155, G.158, G.159, H.160, L.161, S.215, A.216, N.397 Chain D: E.87, F.94, Y.95, F.306, F.309, P.310 Ligands: GLY.6 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.155, C:L.161, D:F.94, D:F.94, D:Y.95, D:F.306, D:F.306, D:F.309 Hydrogen bonds: C:G.159, C:G.159, C:L.161, C:S.215, C:A.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katinas, J.M. et al., Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2. Biochemistry (2024)

Release Date

2024-03-20

Peptides

Serine hydroxymethyltransferase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Serine hydroxymethyltransferase, mitochondrial

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