SMTL ID : 6wm5.1

Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.224 Hydrogen bonds: A:D.209, A:D.209, A:T.220 Water bridges: A:G.219, A:G.219, A:D.227 FLC.33: 10 residues within 4Å: Chain B: D.169, D.209, G.210, A.213, G.219, T.220, G.223, A.224, D.227 Ligands: NA.36 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.213 Hydrogen bonds: B:D.209, B:T.220, B:G.223 Water bridges: B:D.169, B:G.210, B:G.210, B:G.218

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

NA.2: 4 residues within 4Å: Chain A: D.169, T.220, G.223 Ligands: FLC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.220, 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: 4 residues within 4Å: Chain A: D.206, D.227, D.231 Ligands: NA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.227, A:D.231 Water bridges: A:D.231 NA.5: 3 residues within 4Å: Chain A: R.251, D.252, R.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.253 NA.34: 5 residues within 4Å: Chain B: T.172, D.206, D.209, D.227 Ligands: NA.35 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.206 NA.35: 5 residues within 4Å: Chain B: D.206, D.227, C.230, D.231 Ligands: NA.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.206 Water bridges: B:D.231 NA.36: 5 residues within 4Å: Chain B: D.169, G.219, T.220, G.223 Ligands: FLC.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.169, B:T.220, B:G.223

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 8 residues within 4Å: Chain A: D.235, S.266, I.269, S.270, I.288, E.289, R.290, R.293 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.235, A:S.270, A:S.270, A:I.288, A:R.290 Salt bridges: A:R.293

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

TCE.7: 4 residues within 4Å: Chain A: L.103, L.108, R.163 Ligands: OLC.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.163

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

OLC.8: 6 residues within 4Å: Chain A: P.156, L.157, R.159, A.160, R.163 Ligands: TCE.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.157 Hydrogen bonds: A:R.163 OLC.9: 10 residues within 4Å: Chain A: G.190, L.192, W.245, G.249, M.250, S.304, D.305, P.312, L.315 Ligands: 8K6.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.192, A:W.245 Hydrogen bonds: A:S.304 OLC.10: 10 residues within 4Å: Chain A: D.252, L.254, L.255, P.316, W.320, V.324 Ligands: 8K6.20, 8K6.21, 8K6.24, 8K6.25 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.254, A:W.320, A:W.320, A:V.324 Hydrogen bonds: A:D.252, A:L.255 OLC.11: 7 residues within 4Å: Chain A: F.193, C.197, V.198, F.201, D.305, P.307 Ligands: 8K6.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.198, A:F.201, A:F.201 Hydrogen bonds: A:D.305 OLC.37: 8 residues within 4Å: Chain B: D.252, L.254, L.255, P.316, W.320 Ligands: OLC.38, 8K6.45, 8K6.46 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.320, B:W.320, B:W.320 Hydrogen bonds: B:D.252 OLC.38: 11 residues within 4Å: Chain B: G.190, L.192, W.245, M.250, S.304, D.305, P.312, P.316 Ligands: OLC.37, 8K6.44, 8K6.45 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.316 OLC.39: 2 residues within 4Å: Chain B: G.280, P.341 No protein-ligand interaction detected (PLIP) OLC.40: 11 residues within 4Å: Chain A: R.253, V.257, L.260 Chain B: L.184, P.188, S.240, W.244, F.248, G.249 Ligands: 8K6.14, 8K6.31 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.257, A:L.260, A:L.260, B:L.184, B:P.188, B:P.188, B:W.244, B:W.244, B:W.244 Hydrogen bonds: A:R.253, A:R.253 Salt bridges: A:R.253

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

8K6.12: 7 residues within 4Å: Chain A: D.169, I.173, T.176, T.177, V.180, L.226 Chain B: L.334 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.169, A:I.173, A:T.176, A:L.226, B:L.334 8K6.13: 3 residues within 4Å: Chain A: I.164, L.166 Ligands: 8K6.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.164, A:L.166 8K6.14: 6 residues within 4Å: Chain A: V.327, L.330 Ligands: 8K6.15, 8K6.31, OLC.40, 8K6.41 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.327, A:L.330 8K6.15: 2 residues within 4Å: Chain A: V.327 Ligands: 8K6.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.327 8K6.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 8K6.17: 1 residues within 4Å: Ligands: OLC.11 No protein-ligand interaction detected (PLIP) 8K6.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 8K6.19: 2 residues within 4Å: Chain A: D.86, N.106 No protein-ligand interaction detected (PLIP) 8K6.20: 1 residues within 4Å: Ligands: OLC.10 No protein-ligand interaction detected (PLIP) 8K6.21: 4 residues within 4Å: Chain A: V.321, V.324 Ligands: OLC.10, 8K6.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.321, A:V.324 8K6.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 8K6.23: 6 residues within 4Å: Chain A: G.165, L.166, T.167, A.170, I.174 Ligands: 8K6.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.166, A:T.167, A:A.170 8K6.24: 7 residues within 4Å: Chain A: P.313, P.316, V.317, W.320 Ligands: OLC.9, OLC.10, 8K6.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.313, A:P.316, A:V.317, A:W.320 8K6.25: 3 residues within 4Å: Chain A: W.320, V.327 Ligands: OLC.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.320, A:V.327 8K6.26: 5 residues within 4Å: Chain A: F.193, W.200, I.295, L.298, G.302 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.193, A:W.200, A:I.295 8K6.31: 2 residues within 4Å: Ligands: 8K6.14, OLC.40 No protein-ligand interaction detected (PLIP) 8K6.41: 4 residues within 4Å: Chain B: I.173, T.177, V.180 Ligands: 8K6.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.173, B:V.180 8K6.42: 4 residues within 4Å: Chain B: F.193, C.197, P.307 Ligands: 8K6.43 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.193, B:P.307 8K6.43: 4 residues within 4Å: Chain B: K.191, V.198 Ligands: 8K6.42, GOL.50 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.198 8K6.44: 2 residues within 4Å: Chain B: P.313 Ligands: OLC.38 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.313 8K6.45: 4 residues within 4Å: Chain B: V.321, V.324 Ligands: OLC.37, OLC.38 No protein-ligand interaction detected (PLIP) 8K6.46: 4 residues within 4Å: Chain B: W.320, V.327, I.328 Ligands: OLC.37 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.320, B:V.327, B:I.328 8K6.47: 7 residues within 4Å: Chain B: F.193, A.196, W.200, I.295, L.298, G.302, F.306 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.193, B:A.196, B:W.200, B:W.200, B:I.295, B:F.306 8K6.48: 6 residues within 4Å: Chain B: A.178, A.181, G.182, V.185, V.198 Ligands: GOL.50 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.185, B:V.198

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.27: 1 residues within 4Å: Chain A: M.207 No protein-ligand interaction detected (PLIP) GOL.28: 5 residues within 4Å: Chain A: I.296, V.299, G.300, A.314, A.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.296 GOL.29: 1 residues within 4Å: Chain A: R.214 No protein-ligand interaction detected (PLIP) GOL.32: 4 residues within 4Å: Chain A: R.275, A.278, S.279 Chain B: E.277 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.277, A:R.275, A:R.275 Water bridges: A:S.279 GOL.49: 5 residues within 4Å: Chain A: E.277, A.278, G.280 Chain B: E.277, A.278 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.277 GOL.50: 4 residues within 4Å: Chain B: L.186, K.191 Ligands: 8K6.43, 8K6.48 No protein-ligand interaction detected (PLIP)

1 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

XP4.30: 10 residues within 4Å: Chain A: L.184, P.188, I.233, W.244 Chain B: R.253, L.254, V.257, L.260, T.261, V.264 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.184, A:I.233, A:W.244, B:V.257, B:L.260, B:V.264

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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