SMTL ID : 3vzb.2 (2 other biounits)

Crystal structure of Sphingosine Kinase 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x SQS: (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol(Non-covalent)

SQS.1: 15 residues within 4Å: Chain A: D.77, G.109, L.163, S.164, F.169, I.170, D.174, T.192, L.264, M.268, F.284, F.299, M.302, H.307, G.338 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.169, A:I.170, A:F.284, A:F.299 Hydrogen bonds: A:D.77, A:S.164, A:S.164, A:G.338 Water bridges: A:D.337

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: G.21, G.22, K.23, A.106, G.107, S.108, E.185, R.187 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.22, A:K.23, A:S.108, A:S.108, A:E.185 Salt bridges: A:R.187

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

EDO.3: 6 residues within 4Å: Chain A: E.63, E.64, L.65, G.66, R.90, D.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.63, A:L.65, A:G.66, A:R.90 EDO.4: 3 residues within 4Å: Chain A: E.58, L.59, S.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.62 EDO.5: 3 residues within 4Å: Chain A: R.12, R.67, W.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.12, A:R.67 EDO.6: 5 residues within 4Å: Chain A: P.145, N.147, R.275, C.276, N.353 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.275, A:C.276, A:N.353, A:N.353 EDO.7: 6 residues within 4Å: Chain A: G.107, G.109, N.110, A.111, G.265, S.266 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.109, A:N.110, A:N.110, A:N.110, A:S.266 Water bridges: A:G.265, A:E.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Molecular basis of sphingosine kinase 1 substrate recognition and catalysis. Structure (2013)

Release Date

2013-05-08

Peptides

Sphingosine kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Sphingosine kinase 1

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