SMTL ID : 8tlc.1

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and tri-glutamate AGF347 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-tetramer

Ligands

2 x I6I: N-{4-[4-(2-amino-4-oxo-1,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoyl}-D-gamma-glutamyl-L-gamma-glutamyl-D-glutamic acid(Non-covalent)

I6I.1: 17 residues within 4Å: Chain A: L.155, G.158, G.159, H.160, L.161, Y.165, K.170, I.172, S.215, A.216, I.408, R.414 Chain B: E.87, Y.94, Y.95, F.309, P.310 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.155, A:L.155, A:L.161, A:L.161, A:I.172, A:I.408, B:Y.94, B:Y.95, B:P.310 Hydrogen bonds: A:G.158, A:G.159, A:L.161, A:S.215 Salt bridges: A:K.170 I6I.2: 17 residues within 4Å: Chain C: L.155, G.158, G.159, H.160, L.161, Y.165, K.170, I.172, S.215, A.216, I.408, R.414 Chain D: E.87, Y.94, Y.95, F.309, P.310 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.155, C:L.155, C:L.161, C:L.161, C:I.172, C:I.408, D:Y.94, D:Y.95, D:P.310 Hydrogen bonds: C:G.158, C:G.159, C:L.161, C:Y.165, C:S.215 Salt bridges: C: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

2024-02-21

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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