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

Structure of a phosphatidylinositolphosphate (PIP) synthase from Renibacterium Salmoninarum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.62 Å

Oligo State

homo-dimer

Ligands

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

8K6.1: 2 residues within 4Å: Chain A: L.182, I.183 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.183 8K6.2: 2 residues within 4Å: Chain A: P.186, L.246 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.246 8K6.3: 3 residues within 4Å: Chain A: P.251, T.252, I.255 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.251, A:T.252, A:I.255 8K6.4: 4 residues within 4Å: Chain A: G.163, V.164, S.165 Ligands: 8K6.7 No protein-ligand interaction detected (PLIP) 8K6.5: 2 residues within 4Å: Chain A: V.195, V.199 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.195, A:V.199 8K6.6: 4 residues within 4Å: Chain A: V.169, V.199, S.203 Ligands: 8K6.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.169 8K6.7: 4 residues within 4Å: Chain A: V.164, V.172 Ligands: 8K6.4, 8K6.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.172, A:V.172 8K6.8: 1 residues within 4Å: Chain A: W.192 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.192, A:W.192 8K6.9: 1 residues within 4Å: Chain A: N.141 No protein-ligand interaction detected (PLIP) 8K6.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 8K6.11: 2 residues within 4Å: Chain A: V.171, L.175 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.171, A:L.175 8K6.12: 3 residues within 4Å: Chain A: L.147, A.150, I.151 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.147, A:I.151, A:I.151 8K6.16: 1 residues within 4Å: Chain B: I.242 No protein-ligand interaction detected (PLIP) 8K6.17: 3 residues within 4Å: Chain B: L.182, I.183, M.187 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.183 8K6.18: 6 residues within 4Å: Chain A: S.235 Chain B: I.259, V.262, L.263, L.266, I.326 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.259, B:V.262, B:L.263, B:I.326 8K6.19: 2 residues within 4Å: Chain B: V.199, F.200 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.199, B:F.200 8K6.20: 3 residues within 4Å: Chain B: V.164, V.172, S.203 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.164 8K6.21: 1 residues within 4Å: Chain B: V.317 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.317 8K6.22: 2 residues within 4Å: Chain B: W.309, V.313 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.309, B:W.309, B:V.313 8K6.23: 1 residues within 4Å: Chain B: V.313 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.313

4 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 5 residues within 4Å: Chain A: D.204, D.225, D.229 Ligands: MG.14, 58A.15 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.14: 6 residues within 4Å: Chain A: D.204, D.207, G.208, D.225 Ligands: MG.13, 58A.15 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.204, A:D.204, A:D.207, A:D.225 MG.24: 5 residues within 4Å: Chain B: D.204, D.225, D.229 Ligands: MG.25, 58A.26 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.25: 5 residues within 4Å: Chain B: D.204, D.207, D.225 Ligands: MG.24, 58A.26 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.204, B:D.204, B:D.207, 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(Covalent)

58A.15: 27 residues within 4Å: Chain A: 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, V.297, L.301, L.304 Ligands: MG.13, MG.14 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.201, A:F.202, A:I.205, A:D.207, A:L.301, A:L.304 Hydrogen bonds: A:D.167, A:D.167, A:G.208, A:G.218 Salt bridges: A:R.212, A:R.288 58A.26: 28 residues within 4Å: Chain B: P.166, D.167, T.170, F.191, T.194, T.198, V.201, F.202, D.204, I.205, D.207, G.208, A.211, R.212, E.217, G.218, G.221, A.222, L.224, D.225, D.229, R.288, S.289, V.293, L.296, L.304 Ligands: MG.24, MG.25 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.191, B:T.194, B:F.202, B:F.202, B:I.205, B:D.207, B:V.293, B:L.296, B:L.304 Hydrogen bonds: B:D.167, B:D.167, B:T.170, B:G.208, B:E.217 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
D

B
A

Membrane

We predict this structure to be a membrane protein.
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AF2299 protein,Phosphatidylinositol synthase

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