SMTL ID : 9ent.1

SSX structure of Autotaxin in cryogenic conditions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 9 residues within 4Å: Chain A: L.220, S.224, H.433, P.522, N.523, N.524, G.744, 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, Y.214, K.248, F.249, H.251, W.254, P.258, W.260, I.261, F.274, W.275 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.78, A:L.78, A:F.249, A:H.251, A:W.254, A:W.254, A:W.254, A:P.258, A:I.261, A:F.274, A:F.274, A:F.274

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

SCN.3: 2 residues within 4Å: Chain A: Y.677, K.709 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: D.311, H.315, H.474 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.311, A:D.311, A:H.315, A:H.315, A:H.474 ZN.5: 4 residues within 4Å: Chain A: D.171, T.209, D.358, H.359 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

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.739, N.741, D.743, L.745, R.746, D.747 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.739, A:D.743, A:L.745, A:D.747, H2O.12

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

IOD.7: 2 residues within 4Å: Chain A: Y.684, Q.716 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: R.540, S.846 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.250, H.251, R.252 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: N.665, S.760 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: G.226 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: L.376, T.377 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: G.229, N.230, S.231, R.391 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: K.456, P.457, L.458 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: M.232, Y.233, R.393 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: F.562, L.564, C.566 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: L.788 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: T.634, S.636, A.781, D.782 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: K.495, Y.496, R.535 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain A: K.499 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: F.625, R.746, E.749 Ligand excluded by PLIP

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

NA.22: 3 residues within 4Å: Chain A: Y.669, D.672, M.675 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.672 NA.23: 4 residues within 4Å: Chain A: N.801, D.802, S.804, S.807 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.804 NA.24: 1 residues within 4Å: Chain A: K.588 No protein-ligand interaction detected (PLIP)

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

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2