SMTL ID : 6wmv.1

Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii with evidence of substrate binding

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

1 x LIP: L-MYO-INOSITOL-1-PHOSPHATE(Non-covalent)

LIP.1: 9 residues within 4Å: Chain A: R.232, S.270, K.273, E.289, R.290, P.291, R.333 Chain B: Y.271, R.275 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.273, A:E.289, A:R.290, A:R.333 Water bridges: A:D.231, A:R.232 Salt bridges: A:K.273, B:R.275

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: D.169, T.220, G.223 Ligands: TCE.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.220, A:G.223 NA.3: 5 residues within 4Å: Chain A: T.172, D.206, D.209, D.227 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.227 NA.4: 6 residues within 4Å: Chain A: T.176, D.206, D.227, C.230, D.231 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.176, A:D.227 NA.17: 5 residues within 4Å: Chain B: T.176, D.206, D.227, C.230, D.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.206, B:D.227

1 x TCE: 3,3',3''-phosphanetriyltripropanoic acid(Non-covalent)

TCE.5: 11 residues within 4Å: Chain A: P.168, D.169, D.209, G.210, A.213, G.219, T.220, G.223, A.224, D.227 Ligands: NA.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.213 Hydrogen bonds: A:D.209, A:T.220, A:D.227

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 2 residues within 4Å: Chain A: R.253 Ligands: OLC.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.253 1PE.18: 2 residues within 4Å: Chain B: P.313 Ligands: OLC.22 No protein-ligand interaction detected (PLIP)

7 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

OLC.7: 7 residues within 4Å: Chain A: L.184, P.188, M.189, I.233, S.240, W.244 Chain B: T.265 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.188, A:I.233, A:W.244, B:T.265 OLC.8: 5 residues within 4Å: Chain A: F.308, I.309, A.310, W.311 Ligands: OLC.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.311 Hydrogen bonds: A:F.308 OLC.9: 2 residues within 4Å: Chain A: W.311 Ligands: OLC.8 No protein-ligand interaction detected (PLIP) OLC.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLC.20: 4 residues within 4Å: Chain A: R.221 Chain B: G.280, P.341, D.345 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.345 Water bridges: B:G.280, B:P.341 OLC.21: 11 residues within 4Å: Chain A: R.253, L.260, T.261, V.264 Chain B: L.184, P.188, I.233, W.244, F.248 Ligands: 1PE.6, GOL.25 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.188, B:P.188, B:I.233, B:W.244, A:V.264 Hydrogen bonds: A:R.253, A:R.253 OLC.22: 4 residues within 4Å: Chain B: P.316, V.317, W.320 Ligands: 1PE.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.316, B:V.317, B:W.320

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

8K6.10: 8 residues within 4Å: Chain A: T.167, A.170, I.173, V.180, F.222, L.226 Chain B: L.334 Ligands: 8K6.23 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.170, A:I.173, A:V.180, A:F.222, A:L.226, B:L.334 8K6.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 8K6.12: 2 residues within 4Å: Chain A: L.254, W.320 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.320 8K6.13: 5 residues within 4Å: Chain A: F.193, W.200, I.295, V.303, F.306 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.193, A:W.200, A:I.295, A:V.303, A:F.306 8K6.23: 5 residues within 4Å: Chain B: G.331, L.334, H.335, W.338 Ligands: 8K6.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.334, B:W.338, B:W.338 8K6.24: 6 residues within 4Å: Chain A: L.334 Chain B: I.173, T.177, V.180, V.185 Ligands: GOL.25 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.173, B:T.177, B:V.180, B:V.185, A:L.334

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 1 residues within 4Å: Chain A: E.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.67, A:E.67 GOL.25: 5 residues within 4Å: Chain B: L.184, V.185, M.189 Ligands: OLC.21, 8K6.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.185 GOL.26: 1 residues within 4Å: Chain B: V.198 No protein-ligand interaction detected (PLIP)

1 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.15: 9 residues within 4Å: Chain B: P.168, D.169, T.172, M.207, D.209, G.210, A.213, G.223, D.227 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.169, B:D.169, B:T.172, B:M.207, B:M.207, B:D.209, B:G.210

1 x FLC: CITRATE ANION(Non-covalent)

FLC.16: 8 residues within 4Å: Chain A: Y.271 Chain B: R.232, S.270, K.273, E.289, R.290, R.293, R.333 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.232, B:S.270, B:E.289, B:R.290, B:R.333, B:R.333, A:Y.271, A:Y.271 Salt bridges: B:R.232, B:K.273, B:K.273, B:R.293, B:R.333, B:R.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Belcher Dufrisne, M. et al., Structural and Functional Characterization of Phosphatidylinositol-Phosphate Biosynthesis in Mycobacteria. J.Mol.Biol. (2020)

Release Date

2020-05-27

Peptides

AfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
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AfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion

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