SMTL ID : 1t8u.2 (1 other biounit)

Crystal Structure of human 3-O-Sulfotransferase-3 with bound PAP and tetrasaccharide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

2 x SGN- IDS- SGN- UAP: 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic 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

SGN-IDS-SGN-UAP.1: 23 residues within 4Å: Chain B: K.27, R.32, E.50, H.52, R.56, K.81, P.83, S.84, D.118, Y.119, Q.121, T.122, K.125, R.126, W.149, S.150, A.151, T.233, K.234, R.236 Chain C: S.4 Chain D: K.232 Ligands: NA.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.27, B:R.56, B:R.56, B:D.118, B:Q.121, B:S.84, B:Q.121, B:E.50, B:T.233, B:K.234 Water bridges: B:K.125, B:R.56, D:K.232, D:K.232, B:K.28, B:S.124 Salt bridges: B:K.27, B:R.56, B:K.125, B:K.27, B:H.52, B:K.125, D:K.232, B:R.32, B:K.81, B:K.125, B:K.234, B:R.236, D:K.232 SGN-IDS-SGN-UAP.7: 23 residues within 4Å: Chain A: S.4 Chain B: K.232 Chain D: K.27, R.32, E.50, H.52, R.56, K.81, P.83, S.84, D.118, Y.119, Q.121, T.122, K.125, R.126, W.149, S.150, A.151, T.233, K.234, R.236 Ligands: NA.10 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:K.27, D:R.56, D:R.56, D:D.118, D:Q.121, D:T.122, D:S.84, D:Q.121, D:K.234 Water bridges: D:K.125, D:R.56, B:K.232, B:K.232, D:K.28, D:S.124 Salt bridges: D:K.27, D:R.56, D:K.125, D:K.27, D:H.52, D:K.125, B:K.232, D:R.32, D:K.81, D:K.125, D:K.234, D:R.236, B:K.232

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.27, H.52, P.83, S.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.84 Salt bridges: A:K.27, A:H.52 SO4.8: 4 residues within 4Å: Chain C: K.27, H.52, P.83, S.84 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.84 Salt bridges: C:K.27, C:H.52

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

NA.3: 3 residues within 4Å: Chain A: K.27, D.118, T.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.27, A:D.118, A:T.122, A:T.122 NA.4: 5 residues within 4Å: Chain B: K.27, D.118, T.122 Ligands: SGN-IDS-SGN-UAP.1, SGN-IDS-SGN-UAP.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.27, B:K.27, B:T.122 NA.9: 3 residues within 4Å: Chain C: K.27, D.118, T.122 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.27, C:K.27, C:D.118, C:T.122 NA.10: 5 residues within 4Å: Chain D: K.27, D.118, T.122 Ligands: SGN-IDS-SGN-UAP.7, SGN-IDS-SGN-UAP.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.27, D:D.118, D:D.118, D:T.122, D:T.122

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

A3P.5: 18 residues within 4Å: Chain A: V.26, K.28, G.29, G.30, T.31, R.32, A.33, F.37, R.109, S.117, I.182, F.215, P.216, L.230, K.234, G.235, R.236, H.238 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:K.28, A:G.29, A:G.30, A:T.31, A:T.31, A:T.31, A:R.32, A:R.109, A:R.109, A:S.117, A:P.216, A:G.235, A:R.236 Water bridges: A:K.28, A:T.31, A:A.33, A:K.234, A:G.235, A:R.236, A:R.236 Salt bridges: A:K.28, A:K.81, A:R.109, A:K.234, A:H.238 pi-Stacking: A:F.215 A3P.6: 18 residues within 4Å: Chain B: V.26, K.28, G.29, G.30, T.31, R.32, A.33, F.37, R.109, S.117, I.182, F.215, P.216, L.230, K.234, G.235, R.236, H.238 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:K.28, B:G.29, B:G.30, B:T.31, B:T.31, B:R.32, B:R.109, B:S.117, B:P.216, B:G.235, B:R.236 Water bridges: B:K.28, B:K.28, B:A.33, B:K.234, B:R.236, B:R.236 Salt bridges: B:K.28, B:K.28, B:K.81, B:R.109, B:K.234, B:H.238 pi-Stacking: B:F.215 A3P.11: 18 residues within 4Å: Chain C: V.26, K.28, G.29, G.30, T.31, R.32, A.33, F.37, R.109, S.117, I.182, F.215, P.216, L.230, K.234, G.235, R.236, H.238 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:K.28, C:G.29, C:G.30, C:T.31, C:T.31, C:R.32, C:R.109, C:R.109, C:S.117, C:P.216, C:G.235, C:R.236 Water bridges: C:K.28, C:T.31, C:T.31, C:A.33, C:K.234, C:G.235, C:R.236, C:R.236 Salt bridges: C:K.28, C:K.81, C:R.109, C:K.234, C:H.238 pi-Stacking: C:F.215 A3P.12: 18 residues within 4Å: Chain D: V.26, K.28, G.29, G.30, T.31, R.32, A.33, F.37, R.109, S.117, I.182, F.215, P.216, L.230, K.234, G.235, R.236, H.238 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:K.28, D:G.29, D:G.30, D:T.31, D:T.31, D:T.31, D:R.32, D:R.109, D:S.117, D:P.216, D:G.235, D:R.236 Water bridges: D:K.28, D:K.28, D:A.33, D:K.234, D:R.236, D:R.236 Salt bridges: D:K.28, D:K.28, D:K.81, D:R.109, D:K.234, D:H.238 pi-Stacking: D:F.215

Links

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Citation

Moon, A.F. et al., Structural analysis of the sulfotransferase (3-o-sulfotransferase isoform 3) involved in the biosynthesis of an entry receptor for herpes simplex virus 1. J.Biol.Chem. (2004)

Release Date

2004-08-31

Peptides

heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1

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