SMTL ID : 5t0a.1 (1 other biounit)

Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with bound PAP and heptasaccharide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x BDP- GNS- IDS- 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)-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-BDP-GNS.1: 15 residues within 4Å: Chain A: K.428, K.429, R.445, W.450, L.454, H.455, H.500, A.505, T.506, W.507 Ligands: NPO.3, TLA.17, NA.18, NA.20, CL.23 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.428, A:T.509, A:H.398, A:G.504, A:T.506, A:K.508, A:K.508 Salt bridges: A:K.428, A:R.445, A:K.429 Hydrogen bonds: A:R.445, A:H.500, A:T.506, A:W.507

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.45 Water bridges: A:K.43

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

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

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

A3P.4: 18 residues within 4Å: Chain A: H.398, 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, T.625, R.626, A.627 Ligands: EDO.11 20 PLIP interactions: 20 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:S.496, A:Q.600, A:T.620, A:I.622, A:R.626, A:A.627 Water bridges: A:T.406, A:T.406, A:R.503, A:R.503, A:T.620 Salt bridges: A:H.398, A:K.401, A:R.488

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

EDO.5: 1 residues within 4Å: Chain A: R.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.355 EDO.6: 7 residues within 4Å: Chain A: R.409, V.412, R.413, Q.427, K.428, C.430, F.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.413 EDO.7: 4 residues within 4Å: Chain A: R.488, D.489, S.492, T.625 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.488, A:D.489, A:S.492, A:T.625 EDO.8: 6 residues within 4Å: Chain A: R.555, L.560, C.565, Y.566, R.576 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.555 EDO.9: 4 residues within 4Å: Chain A: Y.18, N.19, D.297, K.298 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.19, A:D.297, A:K.298 Water bridges: A:Y.18, A:N.235, A:K.298 EDO.10: 7 residues within 4Å: Chain A: D.96, A.97, Y.177, I.330, M.331, P.332, N.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.333 Water bridges: A:N.333 EDO.11: 2 residues within 4Å: Chain A: R.626 Ligands: A3P.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.401, A:R.503 EDO.12: 4 residues within 4Å: Chain A: N.577, P.578, L.646, Q.649 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.649 EDO.13: 1 residues within 4Å: Chain A: E.575 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.575 EDO.14: 4 residues within 4Å: Chain A: N.550, N.551, L.580 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.551 Water bridges: A:N.550, A:R.576 EDO.15: 4 residues within 4Å: Chain A: A.22, V.36, T.37, V.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.38

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

TLA.16: 5 residues within 4Å: Chain A: S.271, P.272, N.273, K.274, E.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.274, A:E.275 Water bridges: A:K.274 Salt bridges: A:K.274 TLA.17: 4 residues within 4Å: Chain A: H.500, R.503 Ligands: BDP-GNS-IDS-GNS-BDP-GNS.1, NA.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.500 Salt bridges: A:K.401, A:H.500, A:R.503

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

NA.18: 2 residues within 4Å: Ligands: BDP-GNS-IDS-GNS-BDP-GNS.1, BDP-GNS-IDS-GNS-BDP-GNS.1 No protein-ligand interaction detected (PLIP) NA.19: 2 residues within 4Å: Chain A: N.529, D.532 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.531 NA.20: 2 residues within 4Å: Ligands: BDP-GNS-IDS-GNS-BDP-GNS.1, TLA.17 No protein-ligand interaction detected (PLIP) NA.21: 2 residues within 4Å: Chain A: A.628, V.630 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.628

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

CL.22: 3 residues within 4Å: Chain A: F.599, R.601, K.602 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: K.429, G.449, W.450 Ligands: BDP-GNS-IDS-GNS-BDP-GNS.1 Ligand excluded by PLIP

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
A

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

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