SMTL ID : 5hrt.1

Crystal structure of mouse autotaxin in complex with a DNA aptamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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-(1-3)]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.1: 13 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, N.401, N.402, P.487, N.488, N.489, G.705, L.706, H.792 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.2: 3 residues within 4Å: Chain A: L.341, T.342, N.375 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

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 ZN.4: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Chain B: C.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439, H2O.18

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.5: 5 residues within 4Å: Chain A: D.700, N.702, N.704, L.706, D.708 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.700, A:L.706, H2O.6 CA.19: 2 residues within 4Å: Chain B: G.9, G.25 No protein-ligand interaction detected (PLIP)

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

NA.6: 4 residues within 4Å: Chain A: N.762, D.763, S.765, S.768 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.765, A:S.768 Water bridges: A:S.768

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.8: 3 residues within 4Å: Chain A: Y.630, D.633, M.636 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.630, A:D.633, A:M.636, H2O.15

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: K.386, Y.388, E.764, S.765, E.778, L.779, M.782 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.386, A:Y.388, A:Y.388, A:E.778 GOL.10: 6 residues within 4Å: Chain A: L.558, Y.559, A.742, D.743, K.744, C.745 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.745, A:C.745 Water bridges: A:Y.559 GOL.11: 9 residues within 4Å: Chain A: I.605, G.639, F.640, P.644, Y.645, W.673, T.674, Q.677 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.640, A:F.640, A:Y.645, A:Q.677 GOL.12: 6 residues within 4Å: Chain A: Q.383, F.385, K.386, L.411, E.413 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.386, A:L.411, A:E.413 Water bridges: A:H.384 GOL.13: 2 residues within 4Å: Chain A: E.115, R.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.115, A:R.117 GOL.14: 7 residues within 4Å: Chain A: P.509, L.565, R.788, E.791, G.795, L.796, D.797 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.788, A:R.788, A:E.791, A:L.796 GOL.15: 6 residues within 4Å: Chain A: S.196, M.197, Y.198, V.350, R.358, E.406 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.196, A:R.358, A:R.358, A:E.406, A:E.406 Water bridges: A:R.356 GOL.16: 6 residues within 4Å: Chain A: I.605, T.610, Y.638, F.640, K.670 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.670 GOL.17: 7 residues within 4Å: Chain A: V.412, E.413, R.414, D.442, V.445, M.782 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.414, A:D.442 GOL.18: 5 residues within 4Å: Chain A: N.702, N.704, L.706, I.709, E.712 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.702, A:N.704 Water bridges: A:N.704, A:R.707

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, K. et al., Structural basis for specific inhibition of Autotaxin by a DNA aptamer. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-04-06

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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