SMTL ID : 4ndz.1 (1 other biounit)

Structure of Maltose Binding Protein fusion to 2-O-Sulfotransferase with bound heptasaccharide and PAP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

homo-trimer

Ligands

2 x BDP- GNS- IDR- GNS- BDP- NDG- BDP: beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid

BDP-GNS-IDR-GNS-BDP-NDG-BDP.1: 25 residues within 4Å: Chain A: R.382, P.384, T.389, N.393, Y.396, H.408, N.410, K.413, N.414, H.442, H.444, Y.475, F.478, L.479, Y.485, R.486, L.489, R.491, R.492, R.590 Chain B: E.651, K.652, Y.654, K.656 Ligands: NPO.6 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.393, A:N.410, A:R.590, B:E.651, B:K.652, B:K.652, A:H.444, A:R.486, A:R.590 Salt bridges: A:R.382, A:H.442, B:K.652, A:R.486, A:R.491, A:R.590 BDP-GNS-IDR-GNS-BDP-NDG-BDP.3: 24 residues within 4Å: Chain B: R.382, P.384, T.389, N.393, Y.396, H.408, N.410, K.413, N.414, H.442, H.444, Y.475, L.479, Y.485, R.486, L.489, R.491, R.492, R.590 Chain C: E.651, K.652, Y.654, K.656 Ligands: NPO.8 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:Y.654, C:E.651, C:K.652, C:K.652, B:N.393, B:R.590, B:H.444, B:R.486, B:R.590 Salt bridges: C:K.652, B:R.382, B:H.442, B:R.486, B:R.491, B:R.590

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.2: 16 residues within 4Å: Chain B: N.12, D.14, K.15, E.44, W.62, A.63, D.65, R.66, E.111, E.153, P.154, Y.155, F.156, W.230, W.340, R.344 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.44, B:D.65, B:R.66, B:R.66, B:E.153, B:Y.155, B:R.344 GLC-GLC.4: 15 residues within 4Å: Chain C: N.12, D.14, K.15, W.62, A.63, D.65, R.66, E.111, E.153, P.154, Y.155, F.156, W.230, W.340, R.344 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.65, C:R.66, C:R.66, C:E.153, C:Y.155, C:R.344

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

A3P.5: 18 residues within 4Å: Chain A: K.385, T.386, A.387, S.388, T.389, S.390, R.466, S.474, T.556, L.559, Y.581, S.587, H.588, L.589, R.590, K.591, T.592, K.595 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.385, A:T.386, A:A.387, A:S.388, A:S.388, A:T.389, A:T.389, A:S.390, A:S.474, A:Y.581, A:S.587, A:L.589, A:T.592, A:T.592 Salt bridges: A:K.385, A:R.466, A:K.595 A3P.7: 18 residues within 4Å: Chain B: K.385, T.386, A.387, S.388, T.389, S.390, R.466, S.474, T.556, L.559, Y.581, S.587, H.588, L.589, R.590, K.591, T.592, K.595 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.385, B:T.386, B:A.387, B:S.388, B:S.388, B:T.389, B:T.389, B:T.389, B:S.390, B:S.474, B:Y.581, B:L.589, B:T.592, B:T.592 Salt bridges: B:K.385, B:R.466, B:K.595 A3P.9: 18 residues within 4Å: Chain C: K.385, T.386, A.387, S.388, T.389, S.390, R.466, S.474, T.556, L.559, Y.581, S.587, H.588, L.589, R.590, K.591, T.592, K.595 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:K.385, C:T.386, C:A.387, C:S.388, C:S.388, C:T.389, C:T.389, C:S.390, C:S.474, C:Y.581, C:S.587, C:L.589, C:T.592 Salt bridges: C:K.385, C:R.466, C:K.595

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

NPO.6: 2 residues within 4Å: Chain A: R.492 Ligands: BDP-GNS-IDR-GNS-BDP-NDG-BDP.1 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:R.492 NPO.8: 3 residues within 4Å: Chain B: K.413, R.492 Ligands: BDP-GNS-IDR-GNS-BDP-NDG-BDP.3 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:R.492

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Deciphering the role of 2-O-sulfotransferase in regulating heparan sulfate biosynthesis. To be Published

Release Date

2014-03-19

Peptides

Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1 fusion: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1 fusion

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