SMTL ID : 8gku.1

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF355 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

homo-tetramer

Ligands

2 x ZV1: N-{4-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]-2-fluorobenzoyl}-D-glutamic acid(Non-covalent)

ZV1.1: 19 residues within 4Å: Chain A: L.155, G.158, G.159, H.160, L.161, Y.165, V.169, K.170, I.172, S.215, A.216, R.414 Chain B: E.87, Y.94, Y.95, F.306, F.309, P.310 Ligands: GLY.2 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.155, A:I.172, B:Y.94, B:F.306, B:F.309, B:P.310, B:P.310 Hydrogen bonds: A:G.159, A:G.159, A:L.161, A:S.215, A:A.216, B:Y.94 Water bridges: A:R.414, B:Y.94 Salt bridges: A:K.170 ZV1.5: 19 residues within 4Å: Chain C: L.155, G.158, G.159, H.160, L.161, Y.165, V.169, K.170, I.172, S.215, A.216, R.414 Chain D: E.87, Y.94, Y.95, F.306, F.309, P.310 Ligands: GLY.6 16 PLIP interactions: 7 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:Y.94, D:F.306, D:F.309, D:P.310, D:P.310, C:L.155, C:I.172 Hydrogen bonds: D:Y.94, C:G.159, C:G.159, C:L.161, C:S.215, C:A.216 Water bridges: D:Y.94, C:R.414 Salt bridges: C:K.170

2 x GLY: GLYCINE(Non-covalent)

GLY.2: 10 residues within 4Å: Chain A: S.65, H.160, S.215, H.243, K.269, R.414 Chain B: E.87, Y.95 Ligands: ZV1.1, PLP.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.65, A:H.160, A:S.215, B:E.87, B:Y.95 Salt bridges: A:H.243, A:K.269, A:R.414 GLY.6: 10 residues within 4Å: Chain C: S.65, H.160, S.215, H.243, K.269, R.414 Chain D: E.87, Y.95 Ligands: ZV1.5, PLP.7 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:E.87, D:Y.95, C:S.65, C:H.160, C:S.215 Salt bridges: C:H.243, C:K.269, C:R.414

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

PLP.3: 17 residues within 4Å: Chain A: S.131, G.132, S.133, H.160, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269 Chain B: Y.85, Y.130, G.314, G.315 Ligands: GLY.2 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.160, A:A.242, A:T.266, A:K.269 Hydrogen bonds: A:S.131, A:G.132, A:S.133, A:S.215, A:K.269, B:Y.85, B:Y.130, B:G.314, B:G.315 Salt bridges: A:H.268 pi-Stacking: A:H.160 PLP.4: 15 residues within 4Å: Chain A: Y.85, G.314, G.315 Chain B: S.131, G.132, S.133, N.136, H.160, T.214, S.215, D.240, A.242, H.243, H.268, K.269 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.242, B:K.269 Hydrogen bonds: B:G.132, B:S.133, B:S.133, B:N.136, B:T.214, B:K.269, A:Y.85, A:Y.85, A:Y.130, A:G.315 Salt bridges: B:H.268, B:K.269 pi-Cation interactions: B:H.160 PLP.7: 17 residues within 4Å: Chain C: S.131, G.132, S.133, H.160, T.214, S.215, D.240, A.242, H.243, T.266, H.268, K.269 Chain D: Y.85, Y.130, G.314, G.315 Ligands: GLY.6 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.160, C:A.242, C:T.266, C:K.269 Hydrogen bonds: C:S.131, C:G.132, C:S.133, C:S.215, D:G.314, D:G.315 Salt bridges: C:H.268 pi-Stacking: C:H.160 PLP.8: 15 residues within 4Å: Chain C: Y.85, G.314, G.315 Chain D: S.131, G.132, S.133, N.136, H.160, T.214, S.215, D.240, A.242, H.243, H.268, K.269 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.242, D:K.269 Hydrogen bonds: D:G.132, D:S.133, D:S.133, D:N.136, D:T.214, C:Y.85, C:G.315 Salt bridges: D:H.268, D:K.269 pi-Cation interactions: 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

2024-03-20

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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