SMTL ID : 7p4j.1

Crystal structure of Autotaxin and tetrahydrocannabinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: L.185, H.398, P.487, N.488, N.489, D.708, L.710, H.796 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Ligands: PO4.16 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439 ZN.3: 5 residues within 4Å: Chain A: D.136, T.174, D.323, H.324 Ligands: PO4.16 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.136, A:D.136, A:T.174, A:D.323, A:H.324

1 x TCI: (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromen-1-ol(Non-covalent)

TCI.4: 11 residues within 4Å: Chain A: I.132, F.175, L.178, L.181, W.219, F.238, F.239, Y.271, V.321, M.477 Ligands: 5JK.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.132, A:F.175, A:L.178, A:L.181, A:L.181, A:W.219, A:W.219, A:F.238, A:F.239, A:Y.271, A:V.321 Hydrogen bonds: A:F.238 pi-Stacking: A:F.239

1 x 5JK: 7alpha-hydroxycholesterol(Non-covalent)

5JK.5: 14 residues within 4Å: Chain A: L.43, S.46, Y.179, K.213, F.214, H.216, W.219, P.223, W.225, I.226, F.239, W.240 Ligands: TCI.4, GOL.12 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.43, A:F.214, A:F.214, A:H.216, A:W.219, A:W.219, A:W.219, A:W.219, A:P.223, A:I.226, A:F.239, A:F.239

19 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 2 residues within 4Å: Chain A: R.711, E.714 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: M.197, R.358 Ligand excluded by PLIP IOD.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: K.45, V.242, S.243 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain A: T.290 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: P.422, L.423 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: T.229, G.232 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain A: F.527, D.528, L.529, C.531 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain A: C.94, Q.309 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain A: H.246, S.272, I.296, T.299 Ligand excluded by PLIP IOD.30: 2 residues within 4Å: Chain A: G.352, V.418 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain A: S.601, A.746, D.747 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain A: W.218, G.220 Ligands: IOD.33 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain A: N.402, R.404 Ligands: IOD.32 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain A: K.230 Ligand excluded by PLIP IOD.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.10: 5 residues within 4Å: Chain A: F.644, K.674, W.677, A.678, Q.681 No protein-ligand interaction detected (PLIP) SCN.18: 4 residues within 4Å: Chain A: R.414, K.444, N.446, Y.823 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.446

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 2 residues within 4Å: Chain A: V.101, H.107 No protein-ligand interaction detected (PLIP) GOL.12: 4 residues within 4Å: Chain A: H.216, W.219, G.221 Ligands: 5JK.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.216 Water bridges: A:G.221, A:G.221 GOL.13: 11 residues within 4Å: Chain A: K.390, Q.391, H.392, L.393, P.394, K.395, L.397, H.398, Y.399, A.400, Y.707 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.391, A:L.393, A:K.395, A:Y.399 GOL.14: 6 residues within 4Å: Chain A: K.602, S.690, E.691, R.692, N.693, F.742 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.689, A:N.693 GOL.15: 7 residues within 4Å: Chain A: C.531, T.532, N.615, V.617, C.631, K.635, Y.642 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.532, A:N.615, A:V.617, A:K.635, A:K.635, A:Y.642 GOL.17: 10 residues within 4Å: Chain A: N.475, V.476, D.479, T.491, H.492, G.493, S.494, L.495, N.496, L.499 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.479, A:T.491, A:G.493, A:S.494, A:L.495, A:L.495 Water bridges: A:N.475 GOL.19: 8 residues within 4Å: Chain A: Y.570, L.594, P.701, I.702, F.703, R.711, Y.733, T.798 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.570, A:L.594 Water bridges: A:F.703 GOL.20: 7 residues within 4Å: Chain A: V.412, D.413, R.414, D.442, K.444, V.445, M.786 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.413, A:R.414, A:D.442, A:K.444 Water bridges: A:R.414, A:K.444

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

PO4.16: 10 residues within 4Å: Chain A: D.136, T.174, N.195, L.208, D.276, H.280, H.324, H.439 Ligands: ZN.2, ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.174, A:N.195 Salt bridges: A:H.280, A:H.324, A:H.439

2 x CA: CALCIUM ION(Non-covalent)

CA.36: 5 residues within 4Å: Chain A: D.704, N.706, D.708, L.710, D.712 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.704, A:D.708, A:L.710, A:D.712, H2O.7 CA.37: 3 residues within 4Å: Chain A: Y.634, D.637, M.640 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.634, A:D.637, A:M.640

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

NA.38: 3 residues within 4Å: Chain A: N.215, H.216, R.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.217 Water bridges: A:R.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eymery, M.C. et al., Linking medicinal cannabis to autotaxin-lysophosphatidic acid signaling. Life Sci Alliance (2023)

Release Date

2022-12-28

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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