SMTL ID : 1eji.1

RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

PLG.1: 21 residues within 4Å: Chain A: S.47, S.113, G.114, S.115, N.118, H.142, T.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251, R.396 Chain B: Y.67, Y.77, Y.112, G.296, G.297 Ligands: THF.2 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.224 Hydrogen bonds: A:S.47, A:G.114, A:S.115, A:N.118, A:T.196, A:S.197, A:K.251, B:Y.67, B:Y.112, B:G.297 Water bridges: A:S.113, A:S.113 Salt bridges: A:H.225, A:H.250, A:K.251, A:R.396 pi-Stacking: A:H.142 PLG.3: 21 residues within 4Å: Chain A: Y.67, Y.77, Y.112, G.296, G.297 Chain B: S.47, S.113, G.114, S.115, N.118, H.142, T.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251, R.396 Ligands: THF.4 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.224 Hydrogen bonds: B:S.47, B:S.113, B:G.114, B:S.115, B:N.118, B:T.196, B:S.197, B:H.225, B:K.251, A:Y.77, A:G.297 Salt bridges: B:H.225, B:H.250, B:K.251, B:R.396 pi-Stacking: B:H.142 PLG.5: 21 residues within 4Å: Chain C: S.47, S.113, G.114, S.115, N.118, H.142, H.145, T.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251, R.396 Chain D: Y.67, E.69, Y.77, G.296, G.297 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:H.142, C:A.224, C:T.248 Hydrogen bonds: C:S.47, C:G.114, C:S.115, C:N.118, C:H.142, C:S.197, C:K.251, D:Y.67, D:Y.77, D:G.297 Salt bridges: C:H.250, C:K.251, C:K.251, C:R.396 pi-Stacking: C:H.142 PLG.6: 24 residues within 4Å: Chain C: Y.67, E.69, Y.77, Y.112, G.296, G.297 Chain D: S.47, S.113, G.114, S.115, N.118, H.142, T.144, H.145, T.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251, R.396 Ligands: THF.7 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:H.142, D:A.224, D:T.248 Hydrogen bonds: D:S.47, D:G.114, D:S.115, D:N.118, D:H.142, D:T.196, D:H.225, D:K.251, C:Y.77, C:Y.112, C:G.297 Salt bridges: D:H.225, D:H.250, D:K.251, D:R.396 pi-Stacking: D:H.142 Water bridges: C:E.69, C:E.69

3 x THF: 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID(Non-covalent)

THF.2: 19 residues within 4Å: Chain A: L.137, G.140, G.141, H.142, L.143, F.147, K.152, I.154, S.197, C.198, N.381, A.389, L.390 Chain B: E.69, Y.76, Y.77, S.288, P.292 Ligands: PLG.1 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.137, A:L.143, A:A.389, B:Y.76, B:P.292 Hydrogen bonds: A:G.141, A:H.142, A:L.143, A:S.197, A:N.381 Water bridges: A:A.389, A:A.389, B:Y.76, B:Y.76 Salt bridges: A:K.152 THF.4: 18 residues within 4Å: Chain A: E.69, Y.76, Y.77, P.292 Chain B: L.137, G.140, G.141, H.142, L.143, F.147, K.152, I.154, S.197, C.198, N.381, A.389, R.396 Ligands: PLG.3 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.137, B:L.143, A:Y.76 Hydrogen bonds: B:L.137, B:H.142, B:L.143, B:N.381, B:N.381, B:R.396, A:Y.76, A:Y.76, A:Y.76 Salt bridges: B:K.152 THF.7: 15 residues within 4Å: Chain C: E.69, Y.76, Y.77, F.291 Chain D: L.137, G.141, H.142, L.143, K.152, I.154, S.197, C.198, N.381, R.396 Ligands: PLG.6 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.143 Hydrogen bonds: D:H.142, D:L.143, D:S.197, D:R.396, D:R.396, C:Y.76 Water bridges: D:N.379, D:N.381 Salt bridges: D:K.152 pi-Stacking: C:Y.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szebenyi, D.M. et al., Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers. Biochemistry (2000)

Release Date

2000-11-03

Peptides

SERINE HYDROXYMETHYLTRANSFERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

SERINE HYDROXYMETHYLTRANSFERASE