SMTL ID : 7q00.1

Crystal structure of serine hydroxymethyltransferase, isoform 4 from Arabidopsis thaliana (SHM4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: I.51, E.52, G.55 Chain B: I.51, E.52, G.55 No protein-ligand interaction detected (PLIP) EDO.2: 7 residues within 4Å: Chain B: Y.143, K.149, S.154, F.157, E.158, S.159 Chain C: R.126 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.154, B:S.159, C:R.126, C:R.126 Water bridges: B:K.149 EDO.4: 6 residues within 4Å: Chain C: I.51, E.52, G.55 Chain D: I.51, E.52, G.55 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.52 EDO.5: 8 residues within 4Å: Chain C: M.4, E.5, P.6, V.7, W.10 Chain D: R.250, T.399, S.400 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.250, C:P.6 Water bridges: D:R.250 EDO.6: 4 residues within 4Å: Chain C: H.124, I.155 Chain D: P.123, H.124 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.155 Water bridges: D:P.123 EDO.7: 5 residues within 4Å: Chain D: R.205, E.236, Y.237, R.260, P.265 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.237, D:R.260, D:R.260

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 5 residues within 4Å: Chain B: R.35, A.458, S.459, K.473, D.474 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.35, B:A.458 Water bridges: B:D.474

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogues, I. et al., Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives. Plant Physiol Biochem. (2022)

Release Date

2022-08-24

Peptides

Serine hydroxymethyltransferase 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine hydroxymethyltransferase 4

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