SMTL ID : 5d92.2 (1 other biounit)

Structure of a phosphatidylinositolphosphate (PIP) synthase from Renibacterium Salmoninarum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.62 Å

Oligo State

homo-dimer

Ligands

13 x 8K6: Octadecane(Non-covalent)(Non-functional Binders)

8K6.1: 4 residues within 4Å: Chain A: V.169, V.172, S.203 Ligands: 8K6.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.169, A:V.172 8K6.2: 3 residues within 4Å: Chain A: P.186, I.242 Chain B: I.259 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.186, A:I.242, B:I.259 8K6.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 8K6.4: 1 residues within 4Å: Chain A: L.312 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.312 8K6.5: 2 residues within 4Å: Chain A: V.172 Ligands: 8K6.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.172 8K6.6: 2 residues within 4Å: Chain A: P.154, L.158 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.158 8K6.10: 2 residues within 4Å: Chain B: W.192 Ligands: 8K6.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.192, B:W.192 8K6.11: 3 residues within 4Å: Chain B: W.192, V.195 Ligands: 8K6.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.192, B:W.192, B:V.195 8K6.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 8K6.13: 3 residues within 4Å: Chain B: L.182, I.183 Ligands: 8K6.14 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.183 8K6.14: 1 residues within 4Å: Ligands: 8K6.13 No protein-ligand interaction detected (PLIP) 8K6.15: 2 residues within 4Å: Chain B: V.164 Ligands: 8K6.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.164 8K6.16: 4 residues within 4Å: Chain B: V.164, V.172, S.203 Ligands: 8K6.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.164, B:V.172, B:V.172

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain A: D.204, D.225, D.229 Ligands: MG.8, 58A.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.204, A:D.204, A:D.225, A:D.225, A:D.229 MG.8: 6 residues within 4Å: Chain A: D.204, D.207, G.208, D.225 Ligands: MG.7, 58A.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.204, A:D.204, A:D.207, A:D.225 MG.17: 5 residues within 4Å: Chain B: D.204, D.225, D.229 Ligands: MG.18, 58A.19 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.204, B:D.204, B:D.225, B:D.225, B:D.229 MG.18: 6 residues within 4Å: Chain B: D.204, D.207, G.208, D.225 Ligands: MG.17, 58A.19 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.204, B:D.204, B:D.207, B:D.225

2 x 58A: 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine(Non-covalent)(Covalent)

58A.9: 31 residues within 4Å: Chain A: S.137, G.138, P.166, D.167, T.170, F.191, T.198, V.201, F.202, D.204, I.205, D.207, G.208, A.211, R.212, R.216, E.217, G.218, G.221, A.222, L.224, D.225, D.229, R.288, S.289, V.293, L.296, L.301, L.304 Ligands: MG.7, MG.8 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.191, A:V.201, A:F.202, A:I.205, A:D.207, A:L.296, A:L.301, A:L.304 Hydrogen bonds: A:D.167, A:G.208, A:G.218 Salt bridges: A:R.212, A:R.288 58A.19: 28 residues within 4Å: Chain B: P.166, D.167, T.170, T.198, V.201, F.202, D.204, I.205, D.207, G.208, A.211, R.212, R.216, E.217, G.218, G.221, A.222, L.224, D.225, R.288, S.289, V.293, L.296, V.297, L.301, L.304 Ligands: MG.17, MG.18 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.201, B:F.202, B:D.207, B:V.293, B:L.296, B:L.301, B:L.304 Hydrogen bonds: B:D.167, B:T.170, B:G.208 Salt bridges: B:R.212, B:R.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clarke, O.B. et al., Structural basis for phosphatidylinositol-phosphate biosynthesis. Nat Commun (2015)

Release Date

2015-11-04

Peptides

AF2299 protein,Phosphatidylinositol synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

AF2299 protein,Phosphatidylinositol synthase

Related Entries With Identical Sequence