SMTL ID : 7z3k.1

Autotaxin in complex with orthosteric site-binder CpdA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NAG-BMA.1: 7 residues within 4Å: Chain A: L.165, S.169, G.201, P.467, L.690 Ligands: NAG.2, GOL.23 No protein-ligand interaction detected (PLIP)

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

NAG.2: 14 residues within 4Å: Chain A: L.165, Y.166, E.168, S.169, H.378, P.467, N.468, N.469, D.688, G.689, L.690, H.776 Ligands: NAG-BMA.1, GOL.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.166 Hydrogen bonds: A:P.467, A:N.469 Water bridges: A:S.169, A:S.169, A:N.468, A:N.468

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: D.256, H.260, H.304, M.306, H.419 Ligands: ZN.4, IA0.29 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.256, A:D.256, A:H.260, A:H.419 ZN.4: 8 residues within 4Å: Chain A: D.116, T.154, D.256, H.260, H.304, H.419 Ligands: ZN.3, IA0.29 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.116, A:T.154, A:D.256, A:H.304

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

5JK.5: 20 residues within 4Å: Chain A: L.23, S.26, Y.27, F.155, Y.159, K.193, F.194, H.196, W.199, G.200, G.201, Q.202, P.203, W.205, I.206, F.219, W.220, S.221 Ligands: SCN.15, IA0.29 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.23, A:L.23, A:F.155, A:F.194, A:F.194, A:H.196, A:W.199, A:W.199, A:W.199, A:I.206, A:F.219 Hydrogen bonds: A:W.205

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.684, N.686, D.688, L.690, D.692 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.684, A:D.688, A:L.690, A:D.692, H2O.9

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

IOD.7: 7 residues within 4Å: Chain A: K.153, G.174, N.175, S.176, V.330, L.334, R.336 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: S.176, M.177, Y.178, V.330, R.338 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: P.99, P.108 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: N.195, H.196, R.197 Ligand excluded by PLIP IOD.11: 5 residues within 4Å: Chain A: F.507, L.509, G.510, C.511, P.599 Ligand excluded by PLIP IOD.12: 6 residues within 4Å: Chain A: P.732, L.733, R.788, E.792, I.793, L.796 Ligand excluded by PLIP IOD.13: 6 residues within 4Å: Chain A: T.579, S.581, G.674, P.725, A.726, D.727 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain A: T.552, S.553 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain A: L.321, T.322, T.351, A.355 Ligand excluded by PLIP IOD.34: 3 residues within 4Å: Chain A: A.652, R.655, N.746 Ligand excluded by PLIP IOD.35: 1 residues within 4Å: Chain A: R.291 Ligand excluded by PLIP IOD.36: 5 residues within 4Å: Chain A: H.226, F.250, S.252, I.276, T.279 Ligand excluded by PLIP IOD.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain A: D.67, S.70 Ligand excluded by PLIP IOD.39: 5 residues within 4Å: Chain A: F.624, P.628, Y.629, W.657, Q.661 Ligand excluded by PLIP IOD.40: 4 residues within 4Å: Chain A: F.570, R.691, T.693, E.694 Ligand excluded by PLIP IOD.41: 5 residues within 4Å: Chain A: I.500, H.531, D.600, V.601, L.642 Ligand excluded by PLIP

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

SCN.14: 6 residues within 4Å: Chain A: I.589, T.594, Y.622, F.624, K.654 Ligands: GOL.22 No protein-ligand interaction detected (PLIP) SCN.15: 6 residues within 4Å: Chain A: L.23, W.205, T.217, F.218, F.219 Ligands: 5JK.5 No protein-ligand interaction detected (PLIP) SCN.16: 4 residues within 4Å: Chain A: K.440, Y.441, T.443, R.480 No protein-ligand interaction detected (PLIP) SCN.17: 7 residues within 4Å: Chain A: G.171, F.182, R.197, W.198, G.200, R.383, R.384 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.383, A:R.384 Water bridges: A:R.383 SCN.18: 6 residues within 4Å: Chain A: P.144, K.444, V.445, P.446, P.447 Ligands: GOL.25 No protein-ligand interaction detected (PLIP) SCN.28: 7 residues within 4Å: Chain A: L.391, V.392, D.393, R.394, D.422, V.425, M.766 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.422

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

NA.19: 7 residues within 4Å: Chain A: Y.614, K.615, D.617, K.618, M.620, S.621 Ligands: GOL.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.617 NA.20: 5 residues within 4Å: Chain A: N.746, D.747, S.749, C.750, S.752 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.749, A:S.752

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 4 residues within 4Å: Chain A: P.486, T.487, M.488, Y.790 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.488 Water bridges: A:Y.790 GOL.22: 8 residues within 4Å: Chain A: N.595, Y.614, K.615, S.621, Y.622, K.654 Ligands: SCN.14, NA.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.595 Water bridges: A:D.617, A:M.620 GOL.23: 4 residues within 4Å: Chain A: P.467 Ligands: NAG-BMA.1, NAG-BMA.1, NAG.2 No protein-ligand interaction detected (PLIP) GOL.24: 12 residues within 4Å: Chain A: C.68, L.69, G.72, D.73, C.74, T.76, L.231, L.234, S.238, G.286, Q.289, L.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.68, A:C.74, A:Q.289 GOL.25: 4 residues within 4Å: Chain A: P.144, Y.145, P.447 Ligands: SCN.18 No protein-ligand interaction detected (PLIP) GOL.26: 6 residues within 4Å: Chain A: K.582, S.670, E.671, R.672, N.673, F.722 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.582, A:N.673 GOL.27: 8 residues within 4Å: Chain A: T.314, P.331, G.332, H.397, V.398, A.399, D.404 Ligands: GOL.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.332, A:H.397 Water bridges: A:T.333 GOL.30: 6 residues within 4Å: Chain A: H.260, H.397, F.415, G.417, D.418 Ligands: GOL.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.260, A:D.418, A:D.418 Water bridges: A:K.153 GOL.33: 11 residues within 4Å: Chain A: Y.550, S.567, F.570, L.574, P.681, I.682, F.683, R.691, D.692, T.778, L.780 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.550, A:P.681 Water bridges: A:D.692

1 x IA0: [(2~{S},4~{R})-4-[2-[(3,5-dimethylphenyl)amino]-5,7-dihydropyrrolo[3,4-d]pyrimidin-6-yl]-2-methyl-piperidin-1-yl]-(6-fluoranyl-1~{H}-benzotriazol-5-yl)methanone(Non-covalent)

IA0.29: 27 residues within 4Å: Chain A: I.112, S.114, D.116, K.153, T.154, F.155, L.158, Y.159, L.161, A.162, N.175, L.188, K.193, W.205, F.218, F.219, W.220, A.249, F.250, Y.251, E.253, D.256, H.260, H.419 Ligands: ZN.3, ZN.4, 5JK.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.112, A:T.154, A:F.155, A:L.158, A:F.219 Hydrogen bonds: A:T.154, A:N.175, A:F.218, A:W.220, A:D.256, A:H.260, A:H.419 Water bridges: A:K.153, A:K.153, A:K.153, A:K.153 Salt bridges: A:E.253 pi-Stacking: A:F.219, A:Y.251 Halogen bonds: A:E.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salgado-Polo, F. et al., Autotaxin facilitates selective LPA receptor signaling. Cell Chem Biol (2023)

Release Date

2023-01-25

Peptides

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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