SMTL ID : 4d2e.1 (1 other biounit)

Crystal structure of an integral membrane kinase - v2.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-trimer

Ligands

6 x 78M: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)

78M.1: 11 residues within 4Å: Chain A: W.27, L.30, R.31, W.34, I.35, V.47, L.48, V.51, M.72 Ligands: 78M.2, 78M.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.27, A:L.30, A:W.34, A:V.47, A:V.51 Hydrogen bonds: A:R.31 Water bridges: A:W.34 78M.2: 5 residues within 4Å: Chain A: W.27, R.31, L.48, V.52 Ligands: 78M.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.27, A:L.48, A:V.52 78M.3: 7 residues within 4Å: Chain A: A.55, R.64 Chain B: I.119, I.123 Ligands: 78M.1, 78N.6, 78N.8 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.119, B:I.123, A:A.55 Water bridges: A:R.64 Salt bridges: A:R.64 78M.4: 5 residues within 4Å: Chain A: C.50, I.53, L.57, W.121, G.130 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.53, A:W.121 Hydrogen bonds: A:G.130 78M.9: 10 residues within 4Å: Chain C: E.43, A.46, V.71, V.74, E.78, A.117, V.118, W.121 Ligands: 78M.10, 78N.13 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.46, C:V.71, C:V.74, C:A.117, C:V.118, C:W.121 78M.10: 4 residues within 4Å: Chain C: L.49, I.53 Ligands: 78M.9, 78N.13 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.49, C:L.49, C:I.53

8 x 78N: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)

78N.5: 6 residues within 4Å: Chain A: I.114, I.115, V.118, A.122, I.123, W.126 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.114, A:I.115, A:A.122, A:I.123 78N.6: 14 residues within 4Å: Chain A: I.19, A.22, A.23, S.26 Chain B: S.107, V.110, L.111, I.114, I.115, V.118, I.119 Ligands: 78M.3, 78N.7, 78N.8 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.19, B:L.111, B:I.115, B:V.118, B:I.119 Hydrogen bonds: A:S.26, B:S.107, B:L.111 78N.7: 10 residues within 4Å: Chain B: Q.42, E.43, A.46, V.71, V.74, E.78, I.114, A.117, W.121 Ligands: 78N.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.74, B:A.117, B:W.121, B:W.121 78N.8: 6 residues within 4Å: Chain B: V.118, A.122, I.123, W.126 Ligands: 78M.3, 78N.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.122, B:W.126 Hydrogen bonds: B:I.123 78N.11: 2 residues within 4Å: Chain C: W.126 Ligands: 78N.12 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.126, C:W.126 78N.12: 7 residues within 4Å: Chain B: A.55, A.61, R.64 Chain C: I.123, W.126, S.127 Ligands: 78N.11 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.55, C:I.123, C:W.126 Hydrogen bonds: B:R.64, C:I.123, C:S.127 Salt bridges: B:R.64 78N.13: 8 residues within 4Å: Chain C: C.50, W.56, L.57, D.58, W.121, L.125 Ligands: 78M.9, 78M.10 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.121, C:W.121, C:L.125 Hydrogen bonds: C:W.56, C:D.58 78N.14: 6 residues within 4Å: Chain A: D.116, I.119 Chain C: A.55, D.58, R.64, M.72 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.55, A:I.119 Hydrogen bonds: C:R.64 Salt bridges: C:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boland, C. et al., Cell-Free Expression and in Meso Crystallisation of an Integral Membrane Kinase for Structure Determination. Cell.Mol.Life Sci. (2014)

Release Date

2014-07-23

Peptides

DIACYLGLYCEROL KINASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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DIACYLGLYCEROL KINASE

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