SMTL ID : 8t4o.1

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF347 inhibitor with no glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-tetramer

Ligands

2 x Y5C: 4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoic acid(Non-covalent)

Y5C.1: 14 residues within 4Å: Chain A: L.155, G.158, G.159, H.160, L.161, Y.165, I.172, S.215, A.216 Chain B: E.87, Y.94, Y.95, F.309 Ligands: PLG.2 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.161, A:Y.165, B:Y.94, B:Y.95 Hydrogen bonds: A:G.158, A:G.159, A:G.159, A:L.161, A:S.215 Y5C.4: 14 residues within 4Å: Chain C: L.155, G.158, G.159, H.160, L.161, Y.165, I.172, S.215, A.216 Chain D: E.87, Y.94, Y.95, F.309 Ligands: PLG.5 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.161, C:Y.165, D:Y.94, D:Y.95 Hydrogen bonds: C:G.158, C:G.159, C:G.159, C:L.161, C:Y.165, C:S.215

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

PLG.2: 23 residues within 4Å: Chain A: S.65, 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, R.414 Chain B: Y.85, E.87, Y.95, Y.130, G.314, G.315 Ligands: Y5C.1 21 PLIP interactions: 13 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:A.242 Hydrogen bonds: A:S.65, A:S.131, A:G.132, A:S.133, A:N.136, A:S.215, A:K.269, B:Y.85, B:Y.85, B:Y.85, B:E.87, B:Y.95, B:Y.130, B:G.314, B:G.315 Salt bridges: A:H.243, A:H.268, A:K.269, A:R.414 pi-Stacking: A:H.160 PLG.3: 19 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.214, S.215, D.240, A.242, H.243, H.268, K.269, R.414 19 PLIP interactions: 13 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:H.243, B:K.269, B:K.269, A:Y.85, A:Y.85, A:E.87, A:Y.130, A:G.314, A:G.315 Salt bridges: B:H.243, B:H.268, B:K.269, B:R.414 pi-Stacking: B:H.160 PLG.5: 23 residues within 4Å: Chain C: S.65, 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, R.414 Chain D: Y.85, E.87, Y.95, Y.130, G.314, G.315 Ligands: Y5C.4 19 PLIP interactions: 13 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:A.242 Hydrogen bonds: C:S.65, C:S.131, C:G.132, C:S.133, C:N.136, C:S.215, C:K.269, D:Y.85, D:Y.85, D:E.87, D:Y.95, D:G.314, D:G.315 Salt bridges: C:H.243, C:H.268, C:K.269, C:R.414 pi-Stacking: C:H.160 PLG.6: 19 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.214, S.215, D.240, A.242, H.243, H.268, K.269, R.414 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:A.242 Hydrogen bonds: D:S.65, D:S.131, D:G.132, D:S.133, D:H.243, D:K.269, D:K.269, C:Y.85, C:E.87, C:Y.95, C:G.314, C:G.315 Salt bridges: D:H.243, D:H.268, D:K.269, D:R.414 pi-Stacking: D:H.160

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

2024-02-21

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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