SMTL ID : 6hzn.1

Crystal structure of human dermatan sulfate epimerase 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

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

NAG-NAG.1: 7 residues within 4Å: Chain A: F.457, S.474, W.476, F.564, T.607, Y.624, N.626 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.474, A:S.474

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.2: 13 residues within 4Å: Chain A: K.269, Q.270, F.272, A.273, R.277, M.312, N.314, S.316, V.359, P.360, P.361, P.362, D.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.277, A:D.363, A:D.363

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: V.158, N.161 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.158 Hydrogen bonds: A:N.161 NAG.4: 1 residues within 4Å: Chain A: N.620 No protein-ligand interaction detected (PLIP)

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 4 residues within 4Å: Chain A: H.430, E.448, A.449, N.459 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.430, A:E.448, H2O.1, H2O.1, H2O.1

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 8 residues within 4Å: Chain A: E.33, R.37, S.40, S.41, H.42, D.353, G.354, S.355 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.41, A:G.354, A:S.355 Water bridges: A:R.37 Salt bridges: A:E.33, A:R.37, A:H.42 MES.7: 5 residues within 4Å: Chain A: S.58, S.59, P.60, L.61, E.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.61, A:E.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, M. et al., The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms. Chem Sci (2020)

Release Date

2020-01-22

Peptides

Dermatan-sulfate epimerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dermatan-sulfate epimerase