SMTL ID : 7p4o.1

Crystal structure of Autotaxin and 9(R)-delta6a,10a-THC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 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: 13 residues within 4Å: Chain A: L.185, Y.186, E.188, S.189, G.221, H.398, P.487, N.488, N.489, D.708, G.709, L.710, H.796 No protein-ligand interaction detected (PLIP)

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

5JK.2: 18 residues within 4Å: Chain A: L.43, S.46, Y.47, Y.179, K.213, F.214, H.216, W.219, G.220, G.221, P.223, W.225, I.226, F.239, W.240, S.241, V.242 Ligands: 5K9.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.43, A:L.43, A:F.214, A:F.214, A:H.216, A:W.219, A:W.219, A:I.226, A:F.239

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: D.276, H.280, H.439 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.276, A:H.280, A:H.439, H2O.1, H2O.14 ZN.4: 5 residues within 4Å: Chain A: D.136, G.137, T.174, D.323, H.324 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.136, A:T.174, A:D.323, A:H.324, H2O.1

1 x 5K9: (9~{R},10~{a}~{S})-6,6,9-trimethyl-3-pentyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol(Non-covalent)

5K9.5: 16 residues within 4Å: Chain A: I.132, S.134, F.175, L.178, Y.179, L.181, A.182, W.219, L.224, W.225, F.238, F.239, A.269, Y.271, M.477 Ligands: 5JK.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.132, A:I.132, A:F.175, A:L.178, A:L.178, A:A.182, A:W.219, A:F.238, A:F.239, A:Y.271 Hydrogen bonds: A:F.238

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

SCN.6: 6 residues within 4Å: Chain A: Y.517, P.518, I.576, L.577, Y.578, R.622 No protein-ligand interaction detected (PLIP) SCN.7: 5 residues within 4Å: Chain A: S.628, Q.629, N.630, S.724, S.725 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.9

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: R.209, F.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.209 GOL.10: 1 residues within 4Å: Chain A: Y.426 No protein-ligand interaction detected (PLIP)

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

IOD.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: M.197, R.358 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: L.753, R.808 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: F.644, W.677 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: N.215, H.216, R.217 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: S.601, G.694, A.746, D.747 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: N.402, R.404 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: L.341, T.342 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain A: F.527, L.529, C.531, P.619 Ligand excluded by PLIP

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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