SMTL ID : 6xl8.2 (1 other biounit)

Crystal structure of 3-O-Sulfotransferase isoform 3 in complex with 8mer oligosaccharide with no 6S sulfation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

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

BDP-GNS-IDS-GNS-IDS-GNS-BDP.1: 25 residues within 4Å: Chain A: K.28, R.33, E.37, R.40, G.49, A.50, E.51, H.53, R.57, K.82, P.84, S.85, D.119, Q.122, T.123, K.126, I.130, W.150, S.151, H.229, T.234, K.235, R.237 Ligands: NA.2, NPO.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.40, A:G.49, A:Q.122 Salt bridges: A:R.40, A:R.33, A:K.82, A:K.126, A:K.235, A:R.237 Water bridges: A:R.33, A:R.33, A:E.51, A:T.234

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

NA.2: 5 residues within 4Å: Chain A: K.28, D.119, T.123 Ligands: BDP-GNS-IDS-GNS-IDS-GNS-BDP.1, BDP-GNS-IDS-GNS-IDS-GNS-BDP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.28, A:K.28, A:T.123

1 x NPO: P-NITROPHENOL(Non-functional Binders)

NPO.3: 1 residues within 4Å: Ligands: BDP-GNS-IDS-GNS-IDS-GNS-BDP.1 No protein-ligand interaction detected (PLIP)

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

A3P.4: 17 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, K.235, G.236, R.237, H.239 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.29, A:G.30, A:G.31, A:T.32, A:T.32, A:T.32, A:R.33, A:S.118, A:P.217, A:G.236, A:R.237, A:R.237 Water bridges: 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

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 2 residues within 4Å: Chain A: T.123, K.126 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: R.141, E.245 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: Y.209, F.210, P.217 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: K.160 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: R.141 Ligand excluded by PLIP IOD.10: 0 residues within 4Å: (No contacts) Ligand excluded by 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
B

Heparan sulfate glucosamine 3-O-sulfotransferase 3A1

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