SMTL ID : 9box.1 (1 other biounit)

Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 01: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)glycine

01.1: 19 residues within 4Å: Chain A: S.34, S.100, G.101, S.102, H.129, T.183, S.184, D.209, A.211, H.212, T.235, H.237, K.238, R.383 Chain B: Y.54, Y.64, G.283, G.284 Ligands: FFO.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.211 Hydrogen bonds: A:S.34, A:S.100, A:G.101, A:S.102, A:N.105, A:K.238, B:Y.64, B:G.283, B:G.284 Water bridges: A:S.100, A:S.100 Salt bridges: A:H.212, A:H.237, A:K.238, A:R.383 pi-Stacking: A:H.129 01.3: 20 residues within 4Å: Chain A: Y.54, E.56, Y.64, G.283, G.284 Chain B: S.34, S.100, G.101, S.102, H.129, T.183, S.184, D.209, A.211, H.212, T.235, H.237, K.238, R.383 Ligands: FFO.4 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.211 Hydrogen bonds: B:S.34, B:S.100, B:G.101, B:S.102, B:K.238, A:Y.54, A:E.56, A:G.283, A:G.284 Water bridges: B:S.100, B:S.100, B:N.105 Salt bridges: B:H.212, B:H.237, B:K.238, B:R.383 pi-Stacking: B:H.129

2 x FFO: N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid

FFO.2: 20 residues within 4Å: Chain A: L.124, G.127, G.128, H.129, L.130, Y.134, I.141, S.184, A.185, N.368, T.369, S.375, A.376, I.377 Chain B: E.56, Y.63, Y.64, F.275, F.278 Ligands: 01.1 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.124, A:L.124, A:A.376, A:I.377, B:Y.63, B:F.278 Hydrogen bonds: A:G.127, A:G.128, A:G.128, A:L.130, A:S.184, A:N.368, A:N.368, A:A.376, A:I.377, B:E.56, B:Y.63, B:Y.63, B:Y.63 Water bridges: A:N.366 FFO.4: 21 residues within 4Å: Chain A: E.56, Y.63, Y.64, F.275, F.278, P.279 Chain B: L.124, G.127, G.128, H.129, L.130, Y.134, I.141, S.184, A.185, N.366, N.368, S.375, A.376, I.377 Ligands: 01.3 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.124, B:A.376, B:I.377, A:Y.63, A:F.278 Hydrogen bonds: B:G.128, B:G.128, B:L.130, B:S.184, B:N.368, B:N.368, B:A.376, B:I.377, A:E.56, A:Y.63, A:Y.63, A:Y.64 Water bridges: B:Y.134, B:N.366 Salt bridges: B:K.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drago, V.N. et al., Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function. Chem Sci (2024)

Release Date

2024-08-28

Peptides

Serine hydroxymethyltransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Serine hydroxymethyltransferase, mitochondrial

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