SMTL ID : 6fl5.1

Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 19 residues within 4Å: Chain A: S.109, G.110, S.111, N.114, H.138, H.141, T.192, S.193, D.218, A.220, H.221, T.244, H.246, K.247 Chain B: Y.63, Y.108, G.292, G.293 Ligands: CL.2 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.138, A:K.247 Hydrogen bonds: A:S.109, A:G.110, A:S.111, A:N.114, A:S.193, A:H.221, A:T.244, A:K.247, B:Y.63, B:Y.108, B:G.292, B:G.293 Salt bridges: A:H.246, A:K.247 pi-Stacking: A:H.138 PLP.4: 17 residues within 4Å: Chain A: Y.63, Y.108, G.292, G.293 Chain B: S.109, G.110, S.111, N.114, H.138, H.141, S.193, D.218, A.220, H.221, T.244, H.246, K.247 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.138, B:A.220, B:K.247 Hydrogen bonds: B:S.109, B:G.110, B:S.111, B:N.114, B:S.193, B:T.244, A:Y.63, A:G.292, A:G.293 Salt bridges: B:H.246, B:K.247 pi-Stacking: B:H.138 PLP.5: 18 residues within 4Å: Chain C: S.109, G.110, S.111, N.114, H.138, T.140, H.141, S.193, D.218, A.220, H.221, T.244, H.246, K.247 Chain D: Y.63, Y.108, G.292, G.293 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:H.138, C:K.247 Hydrogen bonds: C:S.109, C:G.110, C:S.111, C:S.111, C:N.114, C:S.193, C:H.221, C:T.244, C:K.247, D:Y.63, D:G.292, D:G.293 Salt bridges: C:H.246, C:K.247 pi-Stacking: C:H.138 PLP.7: 17 residues within 4Å: Chain C: Y.63, G.292, G.293 Chain D: S.109, G.110, S.111, N.114, H.138, H.141, T.192, S.193, D.218, A.220, H.221, T.244, H.246, K.247 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:H.138, D:K.247 Hydrogen bonds: D:S.109, D:G.110, D:S.111, D:N.114, D:S.193, D:T.244, D:T.244, C:Y.63, C:G.293 Salt bridges: D:H.246, D:K.247 pi-Stacking: D:H.138

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: S.43, S.193 Chain B: Y.73 Ligands: PLP.1 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: E.65, Y.73 Chain B: S.43, S.193, R.392 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain C: Y.73 Chain D: S.43, S.193, R.392 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: S.43, S.193, H.221, R.392 Chain D: Y.73 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giardina, G. et al., The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells. FEBS J. (2018)

Release Date

2018-10-10

Peptides

Serine hydroxymethyltransferase, cytosolic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
G

D
J

Serine hydroxymethyltransferase, cytosolic