SMTL ID : 5dlv.1 (1 other biounit)

Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 18 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, G.221, Q.222, K.230, N.401, N.402, P.487, N.488, N.489, D.708, G.709, L.710, H.796 Ligands: SCN.24 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: PO4.19 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439 ZN.3: 6 residues within 4Å: Chain A: D.136, G.137, T.174, D.323, H.324 Ligands: PO4.19 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 CA: CALCIUM ION(Non-covalent)

CA.4: 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

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

IOD.5: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: P.422 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: F.527, L.529, C.531 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: H.246, S.272, T.299 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: L.753 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: M.197, Y.198, R.358 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: S.601, G.694, A.746, D.747 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: G.352, H.417, V.418 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: H.162, P.164, K.464 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: E.714 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: P.466 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain A: S.361 Ligand excluded by PLIP

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

PO4.19: 10 residues within 4Å: Chain A: D.136, K.173, T.174, N.195, D.276, H.280, H.324, H.439 Ligands: ZN.2, ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.174, A:T.174, A:T.174, A:T.174, A:N.195 Salt bridges: A:H.280, A:H.324, A:H.439

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

NA.20: 3 residues within 4Å: Chain A: Y.634, D.637, M.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.637 NA.21: 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.769

1 x 5D5: 2-{[(3alpha,5beta,7alpha,8alpha,14beta,17alpha)-3,7-dihydroxy-24-oxocholan-24-yl]amino}ethanesulfonic acid(Non-covalent)

5D5.22: 10 residues within 4Å: Chain A: L.43, S.46, Y.47, K.213, F.214, H.216, W.219, W.225, S.241, V.242 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.43, A:F.214, A:F.214, A:W.219, A:W.219 Hydrogen bonds: A:S.46, A:V.242 Water bridges: A:S.243 Salt bridges: A:K.213

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

SCN.23: 2 residues within 4Å: Chain A: W.225, F.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.238 SCN.24: 4 residues within 4Å: Chain A: G.191, N.402, R.403 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.25: 3 residues within 4Å: Chain A: E.511, R.565, R.804 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.511, A:R.565, A:R.804 GOL.26: 3 residues within 4Å: Chain A: A.672, R.675, N.766 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.675, A:N.766, A:N.766 Water bridges: A:D.767, A:S.772 GOL.27: 6 residues within 4Å: Chain A: L.341, T.342, N.343, T.371, I.372, A.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.342, A:N.343, A:N.343 GOL.28: 4 residues within 4Å: Chain A: T.371, A.374, A.375, K.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.375, A:K.379, A:K.379 GOL.29: 7 residues within 4Å: Chain A: I.373, T.377, K.386, P.387, Y.388, D.767, E.768 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.377, A:P.387 Water bridges: A:H.392, A:D.767, A:E.768 GOL.30: 7 residues within 4Å: Chain A: G.643, F.644, Y.649, K.674, W.677, A.678, Q.681 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.644, A:F.644, A:Y.649, A:A.678, A:Q.681

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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