SMTL ID : 1rv3.1

E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: S.52, S.202, H.230, R.401 Chain B: Y.72, Y.82 Ligands: PLP.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.52, B:Y.82, B:Y.82, B:Y.82 Salt bridges: A:H.230, A:K.256, A:R.401 PO4.3: 10 residues within 4Å: Chain A: Y.72, Y.82 Chain B: S.52, H.147, S.202, H.230, K.256, R.401 Ligands: GLY.4, PLP.5 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.52, B:S.52, A:Y.72, A:Y.82, A:Y.82 Salt bridges: B:H.230, B:K.256, B:R.401 PO4.6: 7 residues within 4Å: Chain C: S.52, S.202, H.230, R.401 Chain D: Y.72, Y.82 Ligands: PLP.7 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.52, D:Y.72, D:Y.82, D:Y.82 Salt bridges: C:H.230, C:K.256, C:R.401 PO4.8: 10 residues within 4Å: Chain C: Y.72, Y.82 Chain D: S.52, H.147, S.202, H.230, K.256, R.401 Ligands: GLY.9, PLP.10 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.52, D:S.52, D:H.147, C:Y.82, C:Y.82, C:Y.82 Salt bridges: D:H.230, D:K.256, D:R.401

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

PLP.2: 17 residues within 4Å: Chain A: S.118, G.119, S.120, H.147, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256 Chain B: Y.72, Y.117, G.301, G.302 Ligands: PO4.1 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.229, A:K.256 Hydrogen bonds: A:G.119, A:S.120, A:S.120, A:T.201, A:H.230, B:Y.72, B:Y.117, B:G.301, B:G.302 Water bridges: A:S.118, A:R.262 Salt bridges: A:H.255, A:K.256 pi-Stacking: A:H.147 PLP.5: 18 residues within 4Å: Chain A: Y.72, Y.117, G.301, G.302 Chain B: S.118, G.119, S.120, H.147, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256 Ligands: PO4.3, GLY.4 14 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A, 10 interactions with chain B Hydrogen bonds: G.4, A:G.301, A:G.302, B:G.119, B:S.120, B:S.120, B:H.230 Water bridges: A:Y.117, B:R.262 Hydrophobic interactions: B:A.229, B:K.256 Salt bridges: B:H.255, B:K.256 pi-Stacking: B:H.147 PLP.7: 17 residues within 4Å: Chain C: S.118, G.119, S.120, H.147, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256 Chain D: Y.72, Y.117, G.301, G.302 Ligands: PO4.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:A.229, C:K.256 Hydrogen bonds: C:G.119, C:S.120, C:S.120, C:T.201, D:G.301, D:G.302 Water bridges: C:S.118, C:R.262 Salt bridges: C:H.255, C:K.256 pi-Stacking: C:H.147 PLP.10: 18 residues within 4Å: Chain C: Y.72, Y.117, G.301, G.302 Chain D: S.118, G.119, S.120, H.147, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256 Ligands: PO4.8, GLY.9 16 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: D:A.229, D:K.256 Hydrogen bonds: D:G.119, D:S.120, D:S.120, D:H.230, C:Y.72, C:Y.117, C:G.301, C:G.302, G.9 Water bridges: D:S.118, D:R.262 Salt bridges: D:H.255, D:K.256 pi-Stacking: D:H.147

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 9 residues within 4Å: Chain A: Y.72, Y.82 Chain B: S.52, S.202, H.230, K.256, R.401 Ligands: PO4.3, PLP.5 7 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: B:S.52, B:S.202, G.4, A:Y.72 Salt bridges: B:H.230, B:K.256, B:R.401 GLY.9: 9 residues within 4Å: Chain C: Y.72, Y.82 Chain D: S.52, S.202, H.230, K.256, R.401 Ligands: PO4.8, PLP.10 7 PLIP interactions: 5 interactions with chain D, 1 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: D:S.52, D:S.202, G.9, C:Y.82 Salt bridges: D:H.230, D:K.256, D:R.401

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

Related Entries With Identical Sequence