SMTL ID : 2vmy.1

Crystal structure of F351GbsSHMT in complex with Gly and FTHF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 9 residues within 4Å: Chain A: S.31, H.122, H.200, K.226, R.357 Chain B: Y.51, Y.61 Ligands: PLP.2, FFO.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.31, A:K.226, B:Y.61 Salt bridges: A:H.200, A:K.226, A:R.357 GLY.4: 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: FFO.3, PLP.5 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 PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.2: 17 residues within 4Å: Chain A: S.93, G.94, A.95, N.98, 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.1 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.199 Hydrogen bonds: A:G.94, A:A.95, A:N.98, A:H.200, A:K.226, B:Y.51, B:G.256, B:G.257 Salt bridges: A:H.225, A:K.226 pi-Stacking: A:H.122 PLP.5: 17 residues within 4Å: Chain A: Y.51, G.256, G.257 Chain B: S.93, G.94, A.95, H.122, A.171, S.172, D.197, A.199, H.200, T.223, H.225, K.226 Ligands: FFO.3, GLY.4 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.199 Hydrogen bonds: B:S.93, B:G.94, B:A.95, A:G.256, A:G.257 Salt bridges: B:H.225, B:K.226 pi-Stacking: B:H.122

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: 21 residues within 4Å: Chain A: E.53, Y.60, Y.61, K.248, F.251, P.252 Chain B: L.117, G.120, G.121, H.122, L.123, V.129, S.172, A.173, N.341, S.349, P.350, G.351, R.357 Ligands: GLY.4, PLP.5 19 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.123, B:L.123, B:P.350, A:Y.60, A:Y.60, A:F.251 Hydrogen bonds: B:G.121, B:G.121, B:L.123, B:S.172, B:N.341, B:N.341, B:G.351, A:E.53, A:Y.60, A:Y.60, A:Y.60, G.4 Salt bridges: A:K.248 FFO.6: 19 residues within 4Å: Chain A: L.117, G.120, G.121, H.122, L.123, V.129, S.172, A.173, N.339, N.341, S.349, P.350, G.351, R.357 Chain B: E.53, Y.60, Y.61, F.251 Ligands: GLY.1 21 PLIP interactions: 8 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.251, A:L.123, A:L.123, A:P.350, A:P.350 Hydrogen bonds: B:E.53, B:R.58, B:Y.60, B:Y.60, B:Y.60, A:L.117, A:G.121, A:L.123, A:S.172, A:N.339, A:N.341, A:N.341, A:S.349, A:G.351 Salt bridges: B:K.248 pi-Stacking: B:Y.60

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.7: 7 residues within 4Å: Chain A: M.99, F.103, F.131, Y.136, I.254 Chain B: M.99, Q.135 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.103, A:F.131, A:I.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pai, V.R. et al., Structural and Functional Studies of Bacillus Stearothermophilus Serine Hydroxymethyltransferase: The Role of Asn(341), Tyr(60) and Phe(351) in Tetrahydrofolate Binding. Biochem.J. (2009)

Release Date

2008-12-16

Peptides

SERINE HYDROXYMETHYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SERINE HYDROXYMETHYLTRANSFERASE

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