SMTL ID : 5s9l.1

AUTOTAXIN, 4-[3-Oxo-3-(2-oxo-2,3-dihydro-benzooxazol-6-yl)-propyl]-piperazine-1-carboxylic acid 3,5-dichloro-benzyl ester, 1.90A, P212121, Rfree=19.1%

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-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)

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.144, A:T.182, A:D.331, A:H.332 CA.10: 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.17

1 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: Y.642, D.645, M.648 Ligands: ACT.5 6 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, ACT.5, H2O.10, H2O.17

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

ACT.4: 4 residues within 4Å: Chain A: V.420, D.421, R.422, V.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.422 Salt bridges: A:R.422 ACT.5: 4 residues within 4Å: Chain A: Y.642, M.648, S.649 Ligands: K.3 No protein-ligand interaction detected (PLIP) ACT.6: 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

1 x 6ZO: (3,5-dichlorophenyl)methyl 4-[3-oxo-3-(2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)propyl]piperazine-1-carboxylate(Non-covalent)

6ZO.7: 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.182, A:L.216 Hydrogen bonds: A:N.203, A:W.248 pi-Stacking: A:F.247

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: 6ZO.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447

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

NA.9: 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:S.780

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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