SMTL ID : 6xkg.2 (1 other biounit)

Crystal structure of 3-O-Sulfotransferase isoform 3 in complex with 8mer oligosaccharide with 6S sulfation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x BDP- SGN- IDS- SGN- IDS- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid

BDP-SGN-IDS-SGN-IDS-SGN.1: 15 residues within 4Å: Chain A: R.33, G.49, E.51, H.53, R.57, K.82, Q.122, K.126, R.127, S.149, S.151, T.234, K.235 Ligands: NPO.2, EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.33, A:S.151, A:S.151 Water bridges: A:R.33, A:R.33, A:R.33, A:E.51, A:R.57, A:R.127 Salt bridges: A:R.57, A:R.127

1 x NPO: P-NITROPHENOL(Non-covalent)

NPO.2: 3 residues within 4Å: Chain A: G.49 Ligands: BDP-SGN-IDS-SGN-IDS-SGN.1, EDO.6 No protein-ligand interaction detected (PLIP)

1 x A3P: ADENOSINE-3'-5'-DIPHOSPHATE(Non-covalent)

A3P.3: 18 residues within 4Å: Chain A: V.27, K.29, G.30, G.31, T.32, R.33, A.34, F.38, R.110, S.118, I.183, F.216, P.217, L.231, K.235, G.236, R.237, H.239 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.29, A:G.30, A:G.31, A:T.32, A:T.32, A:R.33, A:R.110, A:R.110, A:S.118, A:P.217, A:G.236, A:R.237 Water bridges: A:T.32, A:A.34, A:K.82, A:G.236, A:R.237, A:R.237 Salt bridges: A:K.29, A:K.82, A:R.110, A:K.235, A:H.239 pi-Stacking: A:F.216

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

NA.4: 4 residues within 4Å: Chain A: Y.262, D.268, G.270, W.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.270, A:W.271

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 8 residues within 4Å: Chain A: R.33, L.36, R.40, V.48, G.49, A.50, E.51 Ligands: BDP-SGN-IDS-SGN-IDS-SGN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.33, A:R.40, A:A.50 Water bridges: A:R.33 EDO.6: 1 residues within 4Å: Ligands: NPO.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wander, R. et al., Deciphering the substrate recognition mechanisms of the heparan sulfate 3- O -sulfotransferase-3. Rsc Chem Biol (2021)

Release Date

2021-06-23

Peptides

Heparan sulfate glucosamine 3-O-sulfotransferase 3A1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heparan sulfate glucosamine 3-O-sulfotransferase 3A1

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