SMTL ID : 1ls3.1

Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 19 residues within 4Å: Chain A: S.118, G.119, S.120, P.121, N.123, H.147, H.150, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256 Chain B: Y.72, G.301, G.302 Ligands: GLY.2 18 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.229, A:T.253, A:K.256 Hydrogen bonds: A:G.119, A:S.120, A:N.123, A:T.201, A:H.230, A:K.256, B:G.302, G.2 Water bridges: A:S.118, A:S.118, B:Y.72, B:E.74 Salt bridges: A:H.255, A:K.256 pi-Stacking: A:H.147 PLP.3: 15 residues within 4Å: Chain A: Y.72, 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 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.229, B:K.256 Hydrogen bonds: B:G.119, B:S.120, B:T.201, B:H.230, B:K.256, A:Y.72, A:Y.72, A:G.302 Water bridges: B:S.118, B:S.118 Salt bridges: B:H.255, B:K.256 pi-Stacking: B:H.147 PLP.8: 18 residues within 4Å: Chain C: S.118, G.119, S.120, N.123, H.147, H.150, T.201, S.202, D.227, A.229, H.230, T.253, H.255, K.256 Chain D: Y.72, G.301, G.302 Ligands: GLY.7 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.229, C:T.253, C:K.256 Hydrogen bonds: C:G.119, C:S.120, C:N.123, C:T.201, D:Y.72, D:G.301, D:G.302 Salt bridges: C:H.255, C:K.256 pi-Stacking: C:H.147 PLP.10: 15 residues within 4Å: Chain C: Y.72, 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 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.253, D:K.256 Hydrogen bonds: D:G.119, D:S.120, D:T.201, C:G.302 Salt bridges: D:H.255, D:K.256 pi-Stacking: D:H.147

2 x GLY: GLYCINE(Non-covalent)

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

2 x TGF: 2-[4-(4-{4-[(2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDRO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}-4-CARBOXY-BUTYRYLAM INO)-4-CARBOXY-BUTYRYLAMINO]-PENTANEDIOIC ACID(Non-covalent)

TGF.4: 16 residues within 4Å: Chain A: E.74, Y.81, Y.82, F.296, P.297 Chain B: L.142, G.145, G.146, H.147, L.148, K.156, I.159, S.202, C.203, N.384, L.395 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.148, B:L.148, B:L.395, A:F.296, A:P.297 Hydrogen bonds: B:G.146, B:G.146, B:L.148, B:K.156, B:S.202, B:N.384, A:E.74 Salt bridges: B:K.156 Water bridges: A:Y.82 pi-Stacking: A:Y.81 TGF.11: 21 residues within 4Å: Chain C: E.74, Y.81, Y.82, F.296, P.297 Chain D: L.142, G.145, G.146, H.147, L.148, I.159, S.202, C.203, G.370, N.384, K.385, N.386, A.394, L.395, P.397, R.401 18 PLIP interactions: 5 interactions with chain C, 13 interactions with chain D Hydrophobic interactions: C:Y.81, C:F.296, D:L.148, D:L.148, D:P.397 Hydrogen bonds: C:E.74, C:Y.81, C:Y.82, D:G.145, D:G.146, D:L.148, D:S.202, D:N.384, D:N.386, D:A.394, D:A.394 Water bridges: D:R.401 Salt bridges: D:K.385

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain B: L.208, D.209 No protein-ligand interaction detected (PLIP) GOL.6: 8 residues within 4Å: Chain A: S.66, C.67 Chain B: Y.33, I.36, L.480, P.481, G.482, F.483 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:C.67, B:F.483 GOL.9: 1 residues within 4Å: Chain C: D.183 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.212 GOL.12: 2 residues within 4Å: Chain D: N.207, D.209 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, T.F. et al., Location of the Pteroylpolyglutamate Binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase. J.Biol.Chem. (2003)

Release Date

2003-02-04

Peptides

Serine Hydroxymethyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine Hydroxymethyltransferase