SMTL ID : 5dlw.1

Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA) and lysophosphatidic acid (LPA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-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.1: 17 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, G.221, Q.222, H.398, N.401, N.402, A.486, P.487, N.488, N.489, D.708, L.710, H.796 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.221 Water bridges: A:Q.222, A:P.487

2 x ZN: ZINC ION(Non-covalent)

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

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.9

1 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)

NKP.5: 23 residues within 4Å: Chain A: I.132, D.136, K.173, T.174, F.175, L.178, Y.179, L.181, A.182, N.195, L.208, W.219, W.225, F.239, Y.271, D.276, H.280, H.324, H.439, M.477 Ligands: ZN.2, ZN.3, 5D5.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.132, A:I.132, A:F.175, A:L.178, A:Y.179, A:L.181, A:L.181, A:W.219, A:W.225, A:Y.271 Hydrogen bonds: A:T.174, A:N.195 Salt bridges: A:H.324, A:H.439

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

5D5.6: 14 residues within 4Å: Chain A: L.43, S.46, Y.47, F.175, R.211, K.213, F.214, H.216, W.219, W.225, F.239, V.242, Y.271 Ligands: NKP.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.43, A:F.175, A:F.214, A:W.219, A:W.219, A:F.239, A:F.239, A:V.242 Hydrogen bonds: A:R.211, A:K.213

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

NA.7: 4 residues within 4Å: Chain A: N.766, D.767, S.769, S.772 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.766, A:S.772 NA.8: 3 residues within 4Å: Chain A: Y.634, D.637, M.640 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.640, A:M.640

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

IOD.9: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: L.529, C.531 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: S.601, A.746, D.747 Ligands: GOL.25 Ligand excluded by PLIP IOD.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: H.246, S.272, T.299 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: S.48, C.50 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: L.753 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: M.197, Y.198, R.358 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: R.711, E.714 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: Q.524 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: R.234, G.236 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: G.352, H.417, V.418 Ligand excluded by PLIP

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

SCN.22: 3 residues within 4Å: Chain A: K.464, V.465, P.466 No protein-ligand interaction detected (PLIP) SCN.23: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 7 residues within 4Å: Chain A: L.591, G.626, S.628, Q.629, N.630, S.724, S.725 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.628, A:N.630, A:S.725, A:S.725 GOL.25: 6 residues within 4Å: Chain A: R.559, H.560, T.599, S.601, D.747 Ligands: IOD.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.559, A:D.747 Water bridges: A:H.560, A:S.601, A:S.601

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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