SMTL ID : 8a11.1

Cryo-EM structure of the Human SHMT1-RNA complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

PLP.1: 12 residues within 4Å: Chain A: S.122, G.123, S.124, H.151, T.205, D.231, H.234, H.259, K.260 Chain B: Y.76, G.305, G.306 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:G.305, B:G.306, A:S.122, A:S.122, A:G.123, A:S.124, A:H.151, A:K.260 Hydrophobic interactions: A:H.151, A:K.260 pi-Stacking: A:H.151 PLP.2: 12 residues within 4Å: Chain C: S.122, G.123, S.124, H.151, D.231, A.233, H.234, H.259, K.260 Chain D: Y.76, Y.121, G.306 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:Y.76, D:Y.121, D:G.306, C:G.123, C:S.124 Hydrophobic interactions: C:A.233, C:K.260 Salt bridges: C:H.259 pi-Cation interactions: C:H.151 PLP.3: 14 residues within 4Å: Chain C: Y.76, G.305, G.306 Chain D: S.122, G.123, S.124, H.151, H.154, D.231, H.234, T.257, H.259, K.260, R.266 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:H.151, D:K.260 Hydrogen bonds: D:G.123, D:S.124, D:S.124, D:H.151, D:H.234, D:H.259, D:K.260, D:R.266, C:G.306 Salt bridges: D:H.151, D:K.260 pi-Cation interactions: D:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spizzichino, S. et al., Structure-based mechanism of riboregulation of the metabolic enzyme SHMT1. Mol.Cell (2024)

Release Date

2023-06-14

Peptides

Serine hydroxymethyltransferase, cytosolic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine hydroxymethyltransferase, cytosolic

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