SMTL ID : 5dlt.1

Crystal structure of Autotaxin (ENPP2) with 7-alpha-hydroxycholesterol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 10 residues within 4Å: Chain A: L.185, S.189, H.398, P.487, N.488, N.489, D.708, L.710, H.796 Ligands: GOL.30 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: T.174, D.276, H.280, H.439 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.174, A:D.276, A:H.280, A:H.439, H2O.10 ZN.3: 4 residues within 4Å: Chain A: D.136, T.174, D.323, H.324 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 5JK: 7alpha-hydroxycholesterol(Non-covalent)

5JK.4: 14 residues within 4Å: Chain A: L.43, S.46, Y.47, Y.179, K.213, F.214, H.216, W.219, P.223, W.225, I.226, F.239, W.240 Ligands: SCN.17 11 PLIP interactions: 11 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:W.219, A:I.226, A:F.239 Water bridges: A:W.225

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.13

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

IOD.6: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: M.197, Y.198, V.350, R.358 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: C.121, F.125, V.126, R.127, P.128 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.215, H.216, R.217 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: P.381 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: L.529, P.619 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: N.541, N.547 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: L.753 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: S.601, A.746, D.747 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: R.505, Y.810, S.811 Ligand excluded by PLIP

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

SCN.16: 3 residues within 4Å: Chain A: Y.642, F.644, K.674 No protein-ligand interaction detected (PLIP) SCN.17: 5 residues within 4Å: Chain A: W.225, G.236, F.238, F.239 Ligands: 5JK.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.238 SCN.18: 4 residues within 4Å: Chain A: K.45, S.46, V.242, S.243 No protein-ligand interaction detected (PLIP) SCN.19: 6 residues within 4Å: Chain A: H.246, F.270, S.272, E.295, I.296, T.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.246, A:S.272 SCN.20: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 No protein-ligand interaction detected (PLIP) SCN.21: 6 residues within 4Å: Chain A: H.190, G.191, R.217, W.218, G.220, R.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.404, A:R.404 SCN.22: 3 residues within 4Å: Chain A: T.572, S.573, I.589 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.573 SCN.23: 4 residues within 4Å: Chain A: P.164, K.464, V.465, P.466 No protein-ligand interaction detected (PLIP) SCN.24: 5 residues within 4Å: Chain A: K.45, S.48, S.49, C.50, D.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.45 SCN.25: 3 residues within 4Å: Chain A: R.711, T.713, E.714 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.714 SCN.35: 5 residues within 4Å: Chain A: V.412, D.413, R.414, D.442, V.445 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.414 Water bridges: A:D.442

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

NA.26: 4 residues within 4Å: Chain A: Y.634, D.637, M.640 Ligands: GOL.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.637, A:M.640 NA.27: 4 residues within 4Å: Chain A: N.766, D.767, S.769, S.772 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.772

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 4 residues within 4Å: Chain A: P.506, T.507, M.508, Y.810 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.508 Water bridges: A:Y.810 GOL.29: 6 residues within 4Å: Chain A: Y.634, K.635, M.640, S.641, Y.642 Ligands: NA.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.640, A:K.674 Water bridges: A:C.631, A:K.635 GOL.30: 3 residues within 4Å: Chain A: P.487 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) GOL.31: 9 residues within 4Å: Chain A: C.88, G.92, D.93, C.94, L.251, L.254, G.306, Q.309, L.310 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.92, A:C.94, A:C.94, A:G.306, A:Q.309 GOL.32: 3 residues within 4Å: Chain A: P.164, Y.165, P.467 No protein-ligand interaction detected (PLIP) GOL.33: 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:S.690, A:N.693 GOL.34: 6 residues within 4Å: Chain A: P.351, G.352, H.417, V.418, A.419, D.424 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.418 Water bridges: A:H.417, A:H.417, A:D.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keune, W.J. et al., Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling. Nat Commun (2016)

Release Date

2016-04-13

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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