SMTL ID : 3vzb.1 (2 other biounits)

Crystal structure of Sphingosine Kinase 1

Coordinates

PDB Format Compare

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: 14 residues within 4Å: Chain A: L.163, S.164, F.169, I.170, V.173, D.174, F.188, T.192, L.257, L.264, M.268, F.284, F.299, H.307 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.169, A:I.170, A:V.173, A:F.188, A:L.257, A:F.284, A:F.299 Hydrogen bonds: A:S.164, A:S.164 Water bridges: A:D.337, A:G.338

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

SO4.2: 7 residues within 4Å: Chain A: G.21, G.22, K.23, A.106, G.107, S.108, R.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.22, A:K.23, A:S.108, A:S.108

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

EDO.3: 7 residues within 4Å: Chain A: C.102, S.103, L.104, L.116, C.134, M.357, V.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.103, A:V.358 EDO.4: 7 residues within 4Å: Chain A: L.209, V.214, G.215, K.217, T.218, H.233, H.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.213, A:G.215, A:H.233 Water bridges: A:H.233, A:H.244 EDO.5: 7 residues within 4Å: Chain A: T.153, A.154, S.155, K.331, V.342, S.343, E.344 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.154, A:S.155, A:K.331, A:V.342, A:E.344 EDO.6: 7 residues within 4Å: Chain A: W.167, G.168, A.171, D.172, Y.202, G.332, V.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.168, A:G.168, A:V.333 EDO.7: 6 residues within 4Å: Chain A: M.146, N.147, L.260, H.261, R.275, C.276 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.147, A:R.275, A:C.276 Water bridges: A:Y.119, A:N.147 EDO.8: 4 residues within 4Å: Chain A: H.118, Y.119, G.274, R.275 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.118, A:Y.119, A:R.275

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
A

Sphingosine kinase 1

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