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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x BDP- SGN- IDS- SGN- IDS- SGN- BDP- NGY: 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic 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)-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-BDP-NGY.1: 33 residues within 4Å: Chain A: K.28, R.33, E.37, R.40, R.46, G.49, A.50, E.51, H.53, R.57, K.82, P.84, S.85, D.119, Y.120, Q.122, T.123, K.126, I.130, P.131, W.150, S.151, A.222, E.223, G.224, H.229, L.231, G.232, T.234, K.235, R.237 Ligands: NPO.2, NA.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.33, A:E.37, A:R.40, A:R.46, A:G.224, A:G.232 Water bridges: A:K.29, A:R.33, A:E.51, A:K.82, A:K.82, A:S.125, A:R.237, A:R.40, A:R.40, A:E.223, A:R.33 Salt bridges: A:R.33, A:K.82, A:K.126, A:K.235, A:R.237, A:R.40 Hydrophobic interactions: A:A.222

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

NPO.2: 2 residues within 4Å: Chain A: R.127 Ligands: BDP-SGN-IDS-SGN-IDS-SGN-BDP-NGY.1 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:R.127

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 25 PLIP interactions: 25 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:R.110, A:S.118, A:P.217, A:G.236, A:R.237 Water bridges: A:K.29, A:A.34, A:K.82, A:K.235, 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: 5 residues within 4Å: Chain A: K.28, D.119, T.123 Ligands: BDP-SGN-IDS-SGN-IDS-SGN-BDP-NGY.1, BDP-SGN-IDS-SGN-IDS-SGN-BDP-NGY.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.28, A:K.28, A:D.119, A:T.123

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

EDO.5: 4 residues within 4Å: Chain A: D.13, G.15, L.74, D.75 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.13, A:D.13, A:D.75, A:D.75 EDO.6: 3 residues within 4Å: Chain A: F.208, Y.209, F.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.208 EDO.7: 5 residues within 4Å: Chain A: L.175, F.176, R.181, E.189, R.192 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.175 Hydrogen bonds: A:R.181, A:E.189 EDO.8: 3 residues within 4Å: Chain A: I.78, K.104, L.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.104 EDO.9: 2 residues within 4Å: Chain A: Y.209, F.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.210

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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