SMTL ID : 1kl2.1

Crystal Structure of Serine Hydroxymethyltransferase Complexed with Glycine and 5-formyl tetrahydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: S.93, G.94, A.95, H.122, A.171, S.172, D.197, A.199, H.200, T.223, H.225, K.226 Chain B: Y.51, G.256, G.257 Ligands: GLY.2 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:Y.51, B:G.256, B:G.257, A:G.94, A:A.95, A:H.200 Hydrophobic interactions: A:H.122, A:A.199, A:T.223 Water bridges: A:N.98 Salt bridges: A:H.225, A:K.226 pi-Stacking: A:H.122 PLP.4: 18 residues within 4Å: Chain A: Y.51, G.256, G.257 Chain B: S.93, G.94, A.95, N.98, H.122, H.125, A.171, S.172, D.197, A.199, H.200, T.223, H.225, K.226 Ligands: GLY.5 15 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:H.122, B:T.223 Hydrogen bonds: B:G.94, B:A.95, B:S.172, B:H.200, A:G.257, G.5 Water bridges: B:N.98, A:E.53, A:G.256, G.5 Salt bridges: B:H.225, B:K.226 pi-Stacking: B:H.122

2 x GLY: GLYCINE(Non-covalent)

GLY.2: 10 residues within 4Å: Chain A: S.31, H.122, S.172, H.200, K.226, R.357 Chain B: Y.51, Y.61 Ligands: PLP.1, FON.3 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.61, A:S.31 Salt bridges: A:H.200, A:K.226, A:R.357 GLY.5: 10 residues within 4Å: Chain A: Y.51, Y.61 Chain B: S.31, H.122, S.172, H.200, K.226, R.357 Ligands: PLP.4, FON.6 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.31, B:K.226, A:Y.61, A:Y.61 Salt bridges: B:H.200, B:K.226, B:R.357

2 x FON: N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid(Non-covalent)

FON.3: 16 residues within 4Å: Chain A: L.117, G.120, G.121, H.122, L.123, S.172, N.339, N.341, F.351, R.357 Chain B: E.53, R.58, Y.60, Y.61, F.251 Ligands: GLY.2 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.121, A:L.123, A:S.172, A:N.339, A:N.341, A:N.341, B:Y.60 Hydrophobic interactions: B:F.251, B:F.251 Salt bridges: B:R.58 pi-Stacking: B:Y.60 FON.6: 20 residues within 4Å: Chain A: E.53, R.58, Y.60, Y.61, F.251, P.252 Chain B: L.117, G.120, G.121, H.122, L.123, V.129, S.172, N.339, N.341, S.349, P.350, F.351, R.357 Ligands: GLY.5 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.121, B:L.123, B:S.172, B:A.173, B:N.339, B:N.341, B:N.341, B:F.351, A:E.53, A:R.58, A:Y.60, A:Y.60, A:Y.60 Hydrophobic interactions: A:F.251 pi-Stacking: A:Y.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trivedi, V. et al., Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism. J.Biol.Chem. (2002)

Release Date

2002-07-10

Peptides

Serine Hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine Hydroxymethyltransferase

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