SMTL ID : 5s9n.1

AUTOTAXIN, [4-(trifluoromethoxy)phenyl]methyl (3aS,6aS)-2-(1H-benzotriazole-5-carbonyl)-1,3,3a,4,6,6a-hexahydropyrrolo[3,4-c]pyrrole-5-carboxylate, 1.80A, P212121, Rfree=23.3%

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN.1: 14 residues within 4Å: Chain A: L.193, E.196, S.197, H.198, G.228, H.406, N.409, N.410, P.495, N.496, N.497, D.716, L.718, H.804 No protein-ligand interaction detected (PLIP)

1 x YVS: [4-(trifluoromethoxy)phenyl]methyl (3aR,6aS)-5-(1H-benzotriazole-5-carbonyl)hexahydropyrrolo[3,4-c]pyrrole-2(1H)-carboxylate(Non-covalent)

YVS.2: 20 residues within 4Å: Chain A: I.140, S.142, D.144, T.182, F.183, L.186, L.189, A.190, N.203, L.216, W.233, F.246, F.247, W.248, Y.279, D.284, H.288, H.447, M.485 Ligands: ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.182, A:F.183, A:L.216, A:Y.279 Hydrogen bonds: A:T.182, A:N.203, A:W.248

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: YVS.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: Y.642, D.645, M.648 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, H2O.7, H2O.14, H2O.14 CA.5: 5 residues within 4Å: Chain A: D.712, N.714, D.716, L.718, D.720 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.712, A:D.716, A:L.718, A:D.720, H2O.14

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

CL.6: 3 residues within 4Å: Chain A: R.719, T.721, E.722 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, R.364 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.147, S.149, I.835 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: A.680, R.683, N.774 Ligand excluded by PLIP

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

NA.10: 4 residues within 4Å: Chain A: N.774, D.775, S.777, S.780 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.774, A:S.780 Water bridges: A:D.775

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hunziker, D. et al., Crystal Structure of a rat Autotaxin complex. To be published

Release Date

2022-04-13

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

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