SMTL ID : 8gkt.1

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF320 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-tetramer

Ligands

4 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 21 residues within 4Å: Chain A: S.65, S.131, G.132, S.133, H.160, T.162, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269, R.414 Chain B: Y.85, E.87, Y.130, G.314, G.315 Ligands: Y7L.2 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.242 Hydrogen bonds: A:S.65, A:G.132, A:S.133, A:S.133, A:K.269, A:K.269, B:Y.85, B:Y.85, B:E.87, B:Y.130, B:G.314, B:G.315 Water bridges: A:R.275, A:R.275 Salt bridges: A:H.243, A:H.268, A:K.269, A:R.414 pi-Stacking: A:H.160 PLG.3: 21 residues within 4Å: Chain A: Y.85, E.87, Y.95, Y.130, G.314, G.315 Chain B: S.65, S.131, G.132, S.133, H.160, T.162, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269, R.414 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.242 Hydrogen bonds: B:S.65, B:S.131, B:G.132, B:S.133, B:S.215, B:K.269, B:K.269, A:Y.85, A:Y.85, A:E.87, A:Y.130, A:G.314, A:G.315 Water bridges: B:S.131, B:R.275 Salt bridges: B:H.243, B:H.268, B:K.269, B:K.269, B:R.414 pi-Stacking: B:H.160 PLG.5: 21 residues within 4Å: Chain C: S.65, S.131, G.132, S.133, H.160, T.162, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269, R.414 Chain D: Y.85, E.87, Y.130, G.314, G.315 Ligands: Y7L.6 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:A.242 Hydrogen bonds: C:S.65, C:G.132, C:S.133, C:S.133, C:T.266, C:K.269, C:K.269, D:Y.85, D:E.87, D:G.314, D:G.315 Water bridges: C:R.275, C:R.275 Salt bridges: C:H.243, C:H.268, C:K.269, C:R.414 pi-Stacking: C:H.160 PLG.7: 21 residues within 4Å: Chain C: Y.85, E.87, Y.95, Y.130, G.314, G.315 Chain D: S.65, S.131, G.132, S.133, H.160, T.162, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269, R.414 21 PLIP interactions: 6 interactions with chain C, 15 interactions with chain D Hydrogen bonds: C:Y.85, C:E.87, C:Y.95, C:G.314, C:G.315, D:S.65, D:S.131, D:G.132, D:S.133, D:S.215, D:K.269, D:K.269 Water bridges: C:Y.130, D:R.275 Hydrophobic interactions: D:A.242 Salt bridges: D:H.243, D:H.268, D:K.269, D:K.269, D:R.414 pi-Stacking: D:H.160

4 x Y7L: N-{5-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]thiophene-2-carbonyl}-L-glutamic acid(Non-covalent)

Y7L.2: 14 residues within 4Å: Chain A: L.155, G.158, G.159, H.160, L.161, Y.165, K.170, I.172, S.215, R.414 Chain B: E.87, Y.94, F.309 Ligands: PLG.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.161, B:Y.94, B:F.309 Hydrogen bonds: A:L.155, A:G.158, A:G.159, A:L.161 Y7L.4: 18 residues within 4Å: Chain A: E.87, Y.94, Y.95, F.306, F.309, P.310 Chain B: L.155, G.158, G.159, H.160, L.161, Y.165, S.167, V.169, K.170, I.172, S.215, A.216 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.155, B:L.161, B:L.161, B:Y.165, A:Y.94, A:Y.95, A:F.306, A:F.309, A:P.310 Hydrogen bonds: B:G.159, B:G.159, B:L.161, B:S.167, B:S.215 Salt bridges: B:K.170, B:K.170 Y7L.6: 14 residues within 4Å: Chain C: L.155, G.158, G.159, H.160, L.161, Y.165, K.170, I.172, S.215, R.414 Chain D: E.87, Y.94, F.309 Ligands: PLG.5 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.161, D:Y.94, D:F.309 Hydrogen bonds: C:L.155, C:G.158, C:G.159, C:L.161, C:Y.165 Y7L.8: 18 residues within 4Å: Chain C: E.87, Y.94, Y.95, F.306, F.309, P.310 Chain D: L.155, G.158, G.159, H.160, L.161, Y.165, S.167, V.169, K.170, I.172, S.215, A.216 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:Y.94, C:Y.95, C:F.306, C:F.309, C:P.310, D:L.155, D:L.161, D:L.161, D:Y.165 Hydrogen bonds: D:G.159, D:G.159, D:L.161, D:S.167, D:S.215 Salt bridges: D:K.170, D:K.170

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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