SMTL ID : 5ijs.1

Crystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: L.185, S.189, P.487, N.488, N.489, L.710, H.796 No protein-ligand interaction detected (PLIP)

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

5JK.2: 12 residues within 4Å: Chain A: L.43, S.46, Y.179, K.213, F.214, H.216, W.219, P.223, W.225, I.226, F.239, W.240 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.43, A:L.43, A:F.214, A:H.216, A:W.219, A:W.219, A:P.223, A:I.226, A:F.239, A:F.239

2 x ZN: ZINC ION(Non-covalent)

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

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.3

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

IOD.6: 3 residues within 4Å: Chain A: M.197, Y.198, R.358 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: N.215, H.216, R.217 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: G.194, N.195, S.196, L.354, R.356 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: S.601, A.746, D.747 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: P.752, L.753, E.812 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: R.711, E.714 Ligand excluded by PLIP

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

NA.12: 4 residues within 4Å: Chain A: Y.634, D.637, K.638, M.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.637 NA.13: 4 residues within 4Å: Chain A: N.766, D.767, S.769, S.772 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hausmann, J. et al., Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin. J.Struct.Biol. (2016)

Release Date

2016-06-15

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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