SMTL ID : 5s9m.1

AUTOTAXIN, (3,5-dichlorophenyl)methyl (3aS,8aR)-2-(1H-benzotriazole-5-carbonyl)-1,3,3a,4,5,7,8,8a-octahydropyrrolo[3,4-d]azepine-6-carboxylate, 1.80A, P212121, Rfree=21.1%

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- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 13 residues within 4Å: Chain A: L.193, E.196, S.197, H.198, G.228, N.409, N.410, P.495, N.496, N.497, D.716, L.718, H.804 No protein-ligand interaction detected (PLIP)

1 x YV1: (3,5-dichlorophenyl)methyl (3aR,8aS)-2-(1H-benzotriazole-5-carbonyl)octahydropyrrolo[3,4-d]azepine-6(1H)-carboxylate(Non-covalent)

YV1.2: 17 residues within 4Å: Chain A: I.140, S.142, D.144, T.182, F.183, L.186, N.203, L.216, W.233, F.246, F.247, W.248, Y.279, D.284, H.288, H.447 Ligands: ZN.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.183, A:L.186, A:L.216, A:Y.279 Hydrogen bonds: A:N.203, A:W.248 pi-Stacking: A:F.246, A:F.247

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, V.358, L.362, R.364 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.358, A:L.362 Hydrogen bonds: A:N.203, A:S.204 Salt bridges: A:K.181, A:R.364 ACT.4: 5 residues within 4Å: Chain A: V.420, D.421, R.422, D.450, V.453 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.450, A:V.453 Hydrogen bonds: A:R.422 Salt bridges: A:R.422 ACT.5: 4 residues within 4Å: Chain A: G.498, T.499, H.500, R.800 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.500 Water bridges: A:N.483, A:G.498 Salt bridges: A:R.800

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 8 residues within 4Å: Chain A: I.617, Y.650, G.651, F.652, Y.657, K.682, W.685, Q.689 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.652, A:K.682, A:W.685 PG4.7: 5 residues within 4Å: Chain A: K.610, S.698, E.699, N.701, F.750 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.610 Water bridges: A:N.701, A:N.701

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: YV1.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447 ZN.9: 5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: CA.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.144, A:T.182, A:D.331, A:H.332

3 x CA: CALCIUM ION(Non-covalent)

CA.10: 6 residues within 4Å: Chain A: D.144, T.182, D.284, D.331, H.332 Ligands: ZN.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.144, A:D.144, A:T.182, A:D.331, A:H.332 CA.11: 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.10, H2O.16, H2O.17 CA.12: 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.16

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

CL.13: 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.14: 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:S.777, A:S.780 Water bridges: A:N.774

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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