SMTL ID : 5ijq.1

Crystal structure of autotaxin (ENPP2) re-refined

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA.1: 8 residues within 4Å: Chain A: L.185, H.398, P.487, N.488, N.489, D.708, 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 11 PLIP interactions: 11 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:W.219, A:I.226, A:F.239, A:F.239, A:F.239

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

SCN.3: 2 residues within 4Å: Chain A: Y.642, K.674 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.674 SCN.33: 4 residues within 4Å: Chain A: S.141, Y.142, K.145, F.285 No protein-ligand interaction detected (PLIP) SCN.34: 5 residues within 4Å: Chain A: K.45, S.48, S.49, C.50, D.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.45 SCN.35: 4 residues within 4Å: Chain A: Q.274, N.291, P.292, E.295 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Ligands: PO4.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439 ZN.5: 6 residues within 4Å: Chain A: D.136, T.174, D.276, D.323, H.324 Ligands: PO4.6 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 11 residues within 4Å: Chain A: D.136, K.173, T.174, N.195, L.208, D.276, H.280, H.324, H.439 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.174, A:N.195 Salt bridges: A:H.324, A:H.439

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.6

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

IOD.8: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: P.752, L.753 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: F.644, W.677 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: G.352, V.418 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: M.197, R.358 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: K.45, V.242, S.243 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: H.246, S.272, I.296, T.299 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: N.215, H.216, R.217 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: S.601, A.746, D.747 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: E.714 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: M.143, R.157 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: L.543, N.547 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: S.641, P.671, K.674 Ligand excluded by PLIP IOD.23: 5 residues within 4Å: Chain A: C.121, F.125, V.126, R.127, P.128 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: N.630, S.724 Ligand excluded by PLIP IOD.25: 5 residues within 4Å: Chain A: R.217, W.218, G.220, R.404 Ligands: IOD.36 Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain A: T.572 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain A: L.529 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain A: P.381 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: R.139, N.446 Ligand excluded by PLIP IOD.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain A: N.402, R.404 Ligands: IOD.25 Ligand excluded by PLIP

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

NA.31: 4 residues within 4Å: Chain A: Y.634, D.637, M.640 Ligands: GOL.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.637 NA.32: 3 residues within 4Å: Chain A: N.766, S.769, S.772 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.769

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.37: 5 residues within 4Å: Chain A: Y.634, K.635, M.640, S.641 Ligands: NA.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.640

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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