SMTL ID : 5t03.2 (1 other biounit)

Crystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and glucuronic acid containing hexasaccharide substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x BDP- GNS- BDP- GNS- BDP- GNS: 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid

BDP-GNS-BDP-GNS-BDP-GNS.1: 13 residues within 4Å: Chain A: K.429, R.445, G.449, W.450, L.454, H.455, H.500, A.505, T.506, W.507 Ligands: NPO.4, NA.13, TLA.14 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.450, A:H.500, A:T.506, A:W.507 Water bridges: A:T.509, A:T.509, A:H.398, A:R.445, A:H.500, A:G.504, A:K.508, A:K.508 Salt bridges: A:R.445

1 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC.2: 20 residues within 4Å: Chain A: N.13, D.15, K.16, K.43, E.45, E.46, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341, Y.342, R.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.43, A:K.43, A:E.45, A:R.345

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

A3P.3: 20 residues within 4Å: Chain A: H.398, I.399, K.401, T.402, G.403, G.404, T.405, T.406, R.488, S.496, T.597, Q.600, T.620, Q.621, I.622, N.623, T.625, R.626, A.627 Ligands: TLA.15 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:K.401, A:T.402, A:G.403, A:G.404, A:T.405, A:T.405, A:T.406, A:S.496, A:Q.600, A:T.620, A:I.622, A:R.626, A:A.627 Water bridges: A:H.398, A:K.401, A:K.401, A:T.405, A:T.406, A:T.406, A:F.407, A:S.496, A:R.503, A:R.503, A:T.620, A:T.620, A:R.626 Salt bridges: A:H.398, A:K.401, A:R.488

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

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

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

EDO.5: 4 residues within 4Å: Chain A: R.488, S.492, N.623, T.625 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.488, A:S.492, A:T.625, A:T.625 EDO.6: 5 residues within 4Å: Chain A: Y.177, I.330, M.331, P.332, N.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.331, A:N.333 Water bridges: A:R.99, A:N.333 EDO.7: 6 residues within 4Å: Chain A: R.555, L.560, C.565, Y.566, L.568, R.576 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.555 EDO.8: 2 residues within 4Å: Chain A: K.589, F.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.589 Water bridges: A:S.586 EDO.9: 4 residues within 4Å: Chain A: N.577, P.578, L.646, Q.649 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.649, A:Q.649 Water bridges: A:P.578

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: N.572, E.573 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: F.599, Q.600, R.601, K.602 Ligand excluded by PLIP

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

NA.12: 2 residues within 4Å: Chain A: N.529, D.532 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.532 Water bridges: A:N.529 NA.13: 2 residues within 4Å: Ligands: BDP-GNS-BDP-GNS-BDP-GNS.1, TLA.14 No protein-ligand interaction detected (PLIP)

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.14: 4 residues within 4Å: Chain A: H.500, R.503 Ligands: BDP-GNS-BDP-GNS-BDP-GNS.1, NA.13 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.401, A:H.500, A:R.503 Salt bridges: A:H.500, A:R.503, A:R.626 TLA.15: 4 residues within 4Å: Chain A: T.405, T.406, R.409 Ligands: A3P.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.405, A:T.406 Water bridges: A:K.401, A:T.405, A:T.405, A:R.626 Salt bridges: A:K.401, A:R.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Structure Based Substrate Specificity Analysis of Heparan Sulfate 6-O-Sulfotransferases. ACS Chem. Biol. (2017)

Release Date

2017-02-01

Peptides

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

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