SMTL ID : 3vzd.2 (1 other biounit)

Crystal structure of Sphingosine Kinase 1 with inhibitor and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

7 x UUL: 4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol(Non-covalent)

UUL.1: 13 residues within 4Å: Chain A: F.170, I.171, V.174, D.175, F.189, T.193, L.265, M.269, F.285, L.296, F.300, M.303, H.308 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.171, A:I.171, A:I.171, A:V.174, A:F.189, A:L.265, A:F.300 Hydrogen bonds: A:T.193, A:T.193 UUL.2: 11 residues within 4Å: Chain A: F.194, L.197, A.198, R.293, A.294 Chain D: A.198, R.293 Chain E: F.194, L.197, A.198, L.297 6 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: E:F.194, E:L.197, A:F.194, A:F.194, A:L.197, D:A.198 UUL.3: 12 residues within 4Å: Chain B: F.170, I.171, V.174, D.175, F.189, T.193, L.265, M.269, F.285, F.300, M.303, H.308 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.171, B:V.174, B:F.300 Hydrogen bonds: B:T.193, B:T.193 UUL.4: 15 residues within 4Å: Chain C: F.170, I.171, V.174, D.175, F.189, T.193, L.256, L.265, M.269, A.271, F.285, L.296, F.300, M.303, H.308 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.171, C:V.174, C:L.256, C:L.265 Hydrogen bonds: C:T.193, C:T.193 UUL.8: 12 residues within 4Å: Chain D: F.170, I.171, V.174, D.175, F.189, T.193, L.265, M.269, F.285, F.300, M.303, H.308 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.171, D:I.171, D:V.174, D:V.174, D:L.265, D:F.300 Hydrogen bonds: D:T.193 UUL.12: 15 residues within 4Å: Chain E: F.170, I.171, V.174, D.175, F.189, T.193, L.256, L.258, L.265, M.269, F.285, L.296, F.300, M.303, H.308 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:I.171, E:I.171, E:I.171, E:V.174, E:V.174, E:F.189, E:L.256, E:L.258, E:L.265 Hydrogen bonds: E:T.193, E:T.193 Water bridges: E:D.175 UUL.16: 13 residues within 4Å: Chain F: F.170, I.171, V.174, D.175, F.189, T.193, M.269, A.271, F.285, L.296, F.300, M.303, H.308 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:I.171, F:V.174, F:F.189, F:F.300 Hydrogen bonds: F:T.193

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 12 residues within 4Å: Chain C: S.76, G.77, D.78, G.79, L.80, G.108, S.109, G.110, R.182, R.188, E.340 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.76, C:G.77, C:G.79, C:L.80, C:S.109, C:G.110, C:R.188 Water bridges: C:S.76, C:S.76, C:E.340 Salt bridges: C:R.182

3 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain C: G.79, D.338, G.339, E.340 Ligands: POP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.340 MG.10: 5 residues within 4Å: Chain D: G.79, D.338, G.339, E.340 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.340 MG.14: 5 residues within 4Å: Chain E: G.79, D.338, G.339, E.340 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.340

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 7 residues within 4Å: Chain C: R.13, S.45, F.46, T.47, W.69 Chain D: R.53, H.56 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain C: R.53 Chain D: R.13, F.46, T.47, W.69 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain E: R.13, S.45, F.46, T.47, W.69 Chain F: R.53, H.56 Ligand excluded by PLIP

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.9: 19 residues within 4Å: Chain D: N.19, R.21, T.51, E.52, R.53, R.54, S.76, G.77, D.78, G.79, L.80, E.83, G.108, S.109, G.110, R.182, R.188, E.340 Ligands: MG.10 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:R.21, D:T.51, D:T.51, D:R.53, D:N.55, D:G.77, D:G.77, D:G.79, D:L.80, D:E.83, D:S.109, D:S.109, D:G.110, D:E.340, D:E.340 Water bridges: D:H.56 Salt bridges: D:R.182, D:R.182, D:R.188 ADP.13: 19 residues within 4Å: Chain E: N.19, R.21, T.51, E.52, R.53, R.54, S.76, G.77, D.78, G.79, L.80, E.83, G.108, S.109, G.110, R.182, R.188, E.340 Ligands: MG.14 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:R.21, E:G.23, E:T.51, E:G.77, E:G.79, E:L.80, E:E.83, E:E.83, E:S.109, E:S.109, E:S.109, E:G.110, E:E.340 Water bridges: E:H.56 Salt bridges: E:R.182, E:R.182, E:R.188

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

2013-05-01

Peptides

Sphingosine kinase 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

E
E

F
F

Sphingosine kinase 1

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