SMTL ID : 1eqb.2 (1 other biounit)

X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY COMPLEX BETWEEN THE Y65F MUTANT OF E-COLI SERINE HYDROXYMETHYLTRANSFERASE, GLYCINE AND 5-FORMYL TETRAHYDROFOLATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 10 residues within 4Å: Chain A: S.35, H.126, S.175, H.203, K.229, R.363 Chain B: Y.55, F.65 Ligands: PLP.2, FFO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.35, A:K.229 Salt bridges: A:H.203, A:R.363 GLY.4: 10 residues within 4Å: Chain A: Y.55, F.65 Chain B: S.35, H.126, S.175, H.203, K.229, R.363 Ligands: PLP.5, FFO.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.35, B:K.229 Salt bridges: B:H.203, B:R.363

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.2: 18 residues within 4Å: Chain A: S.97, G.98, S.99, N.102, H.126, H.129, F.174, S.175, D.200, A.202, H.203, T.226, H.228, K.229 Chain B: Y.55, G.262, G.263 Ligands: GLY.1 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.126 Hydrogen bonds: A:G.98, A:S.99, A:N.102, A:H.203, B:Y.55, B:G.262, B:G.263 Water bridges: A:S.97, A:S.97, A:R.235 Salt bridges: A:H.228, A:K.229 pi-Stacking: A:H.126 PLP.5: 18 residues within 4Å: Chain A: Y.55, G.262, G.263 Chain B: S.97, G.98, S.99, N.102, H.126, H.129, F.174, S.175, D.200, A.202, H.203, T.226, H.228, K.229 Ligands: GLY.4 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:G.262, A:G.263, B:G.98, B:S.99, B:N.102, B:H.203 Hydrophobic interactions: B:H.126 Water bridges: B:S.99, B:S.99, B:R.235 Salt bridges: B:H.228, B:K.229 pi-Stacking: B:H.126

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(Non-covalent)

FFO.3: 17 residues within 4Å: Chain A: L.121, G.124, G.125, H.126, L.127, V.133, S.175, A.176, N.347, S.355, P.356, F.357, R.363 Chain B: E.57, Y.64, F.257 Ligands: GLY.1 18 PLIP interactions: 5 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:Y.64, B:F.257, A:L.127, A:L.127, A:P.356 Hydrogen bonds: B:E.57, B:Y.64, B:Y.64, A:G.124, A:G.125, A:G.125, A:L.127, A:S.175, A:N.347, A:N.347, A:F.357 Water bridges: A:S.355, A:S.355 FFO.6: 17 residues within 4Å: Chain A: E.57, Y.64, F.257 Chain B: L.121, G.124, G.125, H.126, L.127, V.133, S.175, A.176, N.347, S.355, P.356, F.357, R.363 Ligands: GLY.4 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.127, B:L.127, B:P.356, A:Y.64, A:F.257 Hydrogen bonds: B:G.124, B:G.125, B:G.125, B:L.127, B:S.175, B:N.347, B:N.347, B:F.357, A:E.57, A:Y.64, A:Y.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Contestabile, R. et al., Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase. Biochemistry (2000)

Release Date

2000-04-19

Peptides

SERINE HYDROXYMETHYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

SERINE HYDROXYMETHYLTRANSFERASE

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