SMTL ID : 1rvy.1

E75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

2 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Covalent)

PLG.1: 23 residues within 4Å: Chain A: S.52, S.118, G.119, S.120, N.123, H.147, T.149, H.150, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256, R.401 Chain B: Y.72, Q.74, Y.82, Y.117, G.301, G.302 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:D.227 Hydrogen bonds: A:S.52, A:G.119, A:S.120, A:S.120, A:N.123, A:T.149, A:T.201, A:H.230, B:Y.72, B:Y.82, B:Y.117, B:G.301, B:G.302 Water bridges: A:S.118, B:H.304 Salt bridges: A:H.230, A:H.255, A:K.256, A:R.401 pi-Stacking: A:H.147 PLG.4: 23 residues within 4Å: Chain C: S.52, S.118, G.119, S.120, N.123, H.147, T.149, H.150, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256, R.401 Chain D: Y.72, Q.74, Y.82, Y.117, G.301, G.302 20 PLIP interactions: 4 interactions with chain D, 16 interactions with chain C Hydrogen bonds: D:Y.72, D:Y.72, D:G.301, D:G.302, C:S.52, C:G.119, C:S.120, C:S.120, C:N.123, C:H.147, C:T.201, C:K.256 Hydrophobic interactions: C:D.227 Water bridges: C:S.118, C:S.118 Salt bridges: C:H.230, C:H.255, C:K.256, C:R.401 pi-Stacking: C:H.147

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 10 residues within 4Å: Chain A: Y.72, Q.74, Y.82 Chain B: S.52, H.147, S.202, H.230, K.256, R.401 Ligands: PLP.3 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.52, B:S.52, B:S.202, B:S.202, A:Q.74 Salt bridges: B:H.147, B:H.230, B:K.256, B:R.401 PO4.5: 10 residues within 4Å: Chain C: Y.72, Q.74, Y.82 Chain D: S.52, H.147, S.202, H.230, K.256, R.401 Ligands: PLP.6 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.52, D:S.52, D:S.202, D:S.202, C:Q.74, C:Y.82 Salt bridges: D:H.147, D:H.230, D:K.256, D:R.401

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

PLP.3: 18 residues within 4Å: Chain A: Y.72, Y.117, G.301, G.302 Chain B: S.118, G.119, S.120, N.123, H.147, T.149, H.150, D.227, A.229, H.230, T.253, H.255, K.256 Ligands: PO4.2 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:D.227, B:A.229, B:K.256 Hydrogen bonds: B:S.118, B:G.119, B:S.120, B:S.120, B:N.123, B:T.149, B:T.201, B:H.230, A:Y.72, A:Y.72, A:G.301, A:G.302 Salt bridges: B:H.255 pi-Stacking: B:H.147 PLP.6: 18 residues within 4Å: Chain C: Y.72, Y.117, G.301, G.302 Chain D: S.118, G.119, S.120, N.123, H.147, T.149, H.150, D.227, A.229, H.230, T.253, H.255, K.256 Ligands: PO4.5 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:D.227, D:A.229, D:K.256 Hydrogen bonds: D:S.118, D:G.119, D:S.120, D:S.120, D:N.123, D:T.201, D:K.256, C:Y.72, C:Y.117, C:G.301, C:G.302 Salt bridges: D:H.255 pi-Stacking: D:H.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szebenyi, D.M. et al., Serine Hydroxymethyltransferase: Role of Glu75 and Evidence that Serine Is Cleaved by a Retroaldol Mechanism. Biochemistry (2004)

Release Date

2004-06-15

Peptides

Serine hydroxymethyltransferase, cytosolic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Serine hydroxymethyltransferase, cytosolic

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