SMTL ID : 9eu5.1

SSX structure of Autotaxin at room temperature

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

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

NAG-NAG-NAG.1: 8 residues within 4Å: Chain A: L.220, S.224, H.433, P.522, N.523, N.524, L.745, H.831 No protein-ligand interaction detected (PLIP)

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

5JK.2: 11 residues within 4Å: Chain A: L.78, S.81, Y.214, K.248, F.249, H.251, W.254, P.258, W.260, I.261, F.274 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.249, A:F.249, A:H.251, A:W.254, A:W.254, A:W.254, A:P.258, A:F.274, A:F.274, A:F.274 Water bridges: A:G.256

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Y.669, K.670, D.672, M.675, S.676, Y.677 Ligands: NA.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.672 GOL.5: 1 residues within 4Å: Chain A: N.481 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.481

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 7 residues within 4Å: Chain A: P.199, K.495, T.498, K.499, V.500, P.501, H.532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.495

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.6: 4 residues within 4Å: Chain A: P.429, K.430, I.794, H.822 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.794, A:H.822 ZN.7: 4 residues within 4Å: Chain A: I.737, F.738, R.746, L.832 No protein-ligand interaction detected (PLIP) ZN.8: 5 residues within 4Å: Chain A: G.390, R.391, E.441, I.443, H.444 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.443, A:H.444 ZN.9: 1 residues within 4Å: Chain A: V.184 No protein-ligand interaction detected (PLIP) ZN.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.11: 5 residues within 4Å: Chain A: D.311, H.315, H.359, H.474 Ligands: PO4.33 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.311, A:D.311, A:H.315, A:H.474 ZN.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.13: 2 residues within 4Å: Chain A: D.90, L.94 No protein-ligand interaction detected (PLIP) ZN.14: 5 residues within 4Å: Chain A: D.171, T.209, D.358, H.359 Ligands: PO4.33 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.171, A:T.209, A:D.358, A:H.359

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

IOD.15: 1 residues within 4Å: Chain A: R.393 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: P.457, L.458 Ligand excluded by PLIP IOD.17: 5 residues within 4Å: Chain A: C.413, Q.418, F.420, K.421, C.805 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: N.230, S.231, V.385, R.391 Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain A: P.787, L.788, R.843, E.847 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain A: A.454 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: H.251, R.252 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain A: S.636, P.780, A.781, D.782 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: T.748, E.749 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: P.541, S.846 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: G.226, N.437 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: T.607, S.608 Ligand excluded by PLIP IOD.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.29: 5 residues within 4Å: Chain A: H.281, S.307, E.330, I.331, T.334 Ligand excluded by PLIP

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

NA.30: 5 residues within 4Å: Chain A: Y.669, D.672, K.673, M.675 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.672 NA.31: 4 residues within 4Å: Chain A: N.801, D.802, S.804, S.807 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.802, A:D.802, A:S.807

1 x CA: CALCIUM ION(Non-covalent)

CA.32: 6 residues within 4Å: Chain A: D.739, N.741, D.743, L.745, R.746, D.747 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.739, A:D.743, A:L.745, A:D.747

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.33: 9 residues within 4Å: Chain A: K.208, T.209, N.230, L.243, D.311, H.359, H.474 Ligands: ZN.11, ZN.14 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.209, A:T.209, A:T.209, A:N.230, A:N.230 Salt bridges: A:H.474

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Foos, N. et al., In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry. Iucrj (2024)

Release Date

2024-07-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2