SMTL ID : 4pvf.1

Crystal structure of Homo sapiens holo serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), isoform 3, transcript variant 5, 483 aa, at 2.6 ang. resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: S.55, H.150, S.205, H.233, K.259, R.404 Chain B: Y.75, E.77, Y.85 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.55, A:H.150, A:H.233, A:R.404, A:R.404, B:Y.85 GOL.3: 9 residues within 4Å: Chain A: Y.75, E.77, Y.85 Chain B: S.55, H.150, S.205, H.233, K.259, R.404 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.55, B:S.205, B:H.233, B:R.404, B:R.404, A:E.77, A:Y.85 GOL.4: 9 residues within 4Å: Chain C: S.55, H.150, S.205, H.233, K.259, R.404 Chain D: Y.75, E.77, Y.85 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.55, C:H.150, C:H.233, C:R.404, C:R.404 Water bridges: D:Y.75 GOL.6: 9 residues within 4Å: Chain C: Y.75, E.77, Y.85 Chain D: S.55, H.150, S.205, H.233, K.259, R.404 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:E.77, D:S.55, D:S.205, D:H.233, D:R.404, D:R.404 Water bridges: C:Y.75

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 8 residues within 4Å: Chain A: R.209, L.210, I.211, Y.213, I.234, I.243, P.244, N.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.209, A:I.211, A:Y.213, A:N.358 PEG.5: 8 residues within 4Å: Chain C: R.209, L.210, I.211, Y.213, I.234, I.243, P.244, N.358 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.209, C:I.211, C:N.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giardina, G. et al., How pyridoxal 5'-phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state. Febs J. (2015)

Release Date

2015-01-28

Peptides

Serine hydroxymethyltransferase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Serine hydroxymethyltransferase, mitochondrial