SMTL ID : 5wri.1

Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and C4 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ASP- PHE- GLU- ASP- TYR- GLU- PHE- ASP: ASP-PHE-GLU-ASP-TYR-GLU-PHE-ASP(Non-covalent)

ASP-PHE-GLU-ASP-TYR-GLU-PHE-ASP.1: 20 residues within 4Å: Chain A: P.57, E.79, R.81, R.85, A.88, P.140, F.141, K.144, V.177, T.178, I.179, A.180, F.182, A.197, R.264 Chain B: M.92, W.93, S.96, E.99, R.102 37 PLIP interactions: 31 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.57, A:P.57, A:P.140, A:F.141, A:F.141, A:K.144, A:V.177, A:I.179, A:A.180, A:F.182, A:A.197, B:E.99 Hydrogen bonds: A:E.79, A:R.81, A:R.81, A:K.144, A:K.144, A:T.178, A:T.178, A:T.178, A:T.178, A:A.180, A:A.180, B:S.96, B:R.102 Water bridges: A:R.85, A:R.85, A:R.85, A:I.179, A:R.264, A:R.264, B:E.99, B:E.99 Salt bridges: A:R.85, A:K.144, A:R.264, B:R.102 ASP-PHE-GLU-ASP-TYR-GLU-PHE-ASP.2: 19 residues within 4Å: Chain A: M.92, W.93, S.96, E.99, R.102 Chain B: P.57, E.79, R.81, R.85, P.140, F.141, K.144, V.177, T.178, I.179, A.180, F.182, A.197, R.264 36 PLIP interactions: 30 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:P.57, B:P.57, B:P.140, B:F.141, B:F.141, B:K.144, B:I.179, B:A.180, B:F.182, B:A.197, A:E.99, A:E.99 Hydrogen bonds: B:E.79, B:R.81, B:R.81, B:K.144, B:T.178, B:T.178, B:T.178, B:T.178, B:T.178, B:A.180, B:A.180 Water bridges: B:R.85, B:R.85, B:R.85, B:K.144, B:I.179, B:F.182, B:R.264, A:E.99, A:E.99, A:R.102 Salt bridges: B:R.85, B:R.264, A:R.102

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

A3P.3: 21 residues within 4Å: Chain A: R.58, S.59, G.60, T.61, T.62, L.63, R.163, S.171, R.175, Y.218, V.222, H.247, S.265, Q.268, V.269, K.271, P.272, V.273, N.274, A.277, K.280 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:R.58, A:S.59, A:G.60, A:T.61, A:T.61, A:T.61, A:T.62, A:T.62, A:Y.218, A:S.265, A:P.272, A:N.274 Water bridges: A:R.58, A:L.63, A:A.167, A:S.171, A:S.171, A:S.265, A:N.274, A:N.274 Salt bridges: A:R.58, A:R.58, A:K.138, A:R.163, A:R.175, A:K.280 A3P.6: 20 residues within 4Å: Chain B: R.58, S.59, G.60, T.61, T.62, L.63, R.163, S.171, R.175, Y.218, H.247, S.265, Q.268, V.269, K.271, P.272, V.273, N.274, A.277, K.280 30 PLIP interactions: 30 interactions with chain B Hydrogen bonds: B:R.58, B:S.59, B:G.60, B:T.61, B:T.61, B:T.61, B:T.62, B:S.171, B:Y.218, B:S.265, B:P.272, B:N.274 Water bridges: B:R.58, B:A.167, B:S.171, B:S.171, B:S.174, B:S.265, B:N.274, B:N.274, B:N.274, B:N.274, B:A.277, B:K.280 Salt bridges: B:R.58, B:R.58, B:K.138, B:R.163, B:R.175, B:K.280

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.69, H.71, I.74, G.255 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.69, A:H.71, A:I.74, A:G.255, H2O.2, H2O.3 MG.7: 4 residues within 4Å: Chain B: D.69, H.71, I.74, G.255 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.69, B:H.71, B:I.74, B:G.255, H2O.12, H2O.16

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: M.206, G.209, Y.210 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.206, A:Y.210 Water bridges: A:M.206, A:G.209, A:K.211

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 3 residues within 4Å: Chain B: H.246, E.248, E.249 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.246, B:E.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, S. et al., Structural basis for the broad substrate specificity of the human tyrosylprotein sulfotransferase-1. Sci Rep (2017)

Release Date

2017-09-13

Peptides

Protein-tyrosine sulfotransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein-tyrosine sulfotransferase 1