SMTL ID : 8w5z.1

Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of tick anticoagulant protein madanin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

A3P.1: 19 residues within 4Å: Chain A: R.74, S.75, G.76, T.77, T.78, L.79, R.179, S.187, R.191, Y.234, S.280, Q.283, V.284, K.286, P.287, I.288, N.289, A.292, K.295 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.74, A:S.75, A:G.76, A:T.77, A:T.78, A:T.78, A:T.78, A:S.280, A:P.287, A:N.289, A:N.289 Water bridges: A:T.77, A:L.79, A:K.154, A:A.292 Salt bridges: A:R.74, A:R.74, A:K.154, A:R.179, A:R.191, A:K.295 A3P.12: 19 residues within 4Å: Chain C: R.74, S.75, G.76, T.77, T.78, L.79, R.179, S.187, R.191, Y.234, S.280, Q.283, V.284, K.286, P.287, I.288, N.289, A.292, K.295 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:R.74, C:S.75, C:G.76, C:T.77, C:T.77, C:T.77, C:T.78, C:Y.234, C:S.280, C:P.287, C:N.289, C:N.289 Water bridges: C:R.74, C:L.79, C:S.187, C:T.190, C:S.280, C:A.292 Salt bridges: C:R.74, C:R.74, C:K.154, C:R.179, C:R.191, C:K.295

4 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.2: 8 residues within 4Å: Chain A: Y.218, Y.233, W.244, R.247, Q.317, L.318, G.319 Ligands: 1PS.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.233 Salt bridges: A:R.247 1PS.3: 4 residues within 4Å: Chain A: G.298, I.300, P.301 Ligands: TRS.8 No protein-ligand interaction detected (PLIP) 1PS.6: 8 residues within 4Å: Chain A: Y.233, Q.236, L.318, G.319, Y.320, D.328, Y.329 Ligands: 1PS.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.320 Hydrogen bonds: A:Q.236 pi-Stacking: A:Y.233 1PS.7: 5 residues within 4Å: Chain A: V.163, Y.164, R.167, Q.220, Q.223 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.163, A:R.167 Hydrogen bonds: A:Q.220, A:Q.223

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 5 residues within 4Å: Chain A: L.120, E.121, G.123 Chain C: E.94, L.274 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:L.120, A:E.121, C:E.94, C:L.274 TRS.5: 5 residues within 4Å: Chain A: A.316, G.319, Y.320, D.321, P.322 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.316 Water bridges: A:G.319, A:G.319, A:D.321, A:D.321, A:D.321 TRS.8: 8 residues within 4Å: Chain A: S.201, D.202, Y.203, R.204, P.301, D.303, V.304 Ligands: 1PS.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.203, A:R.204, A:D.303 Water bridges: A:R.204 TRS.9: 6 residues within 4Å: Chain A: E.94, A.273, L.274, S.275 Chain C: L.120, E.121 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.94, A:L.274, C:E.121 Water bridges: A:L.274

4 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 2 residues within 4Å: Chain A: D.333, N.334 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain A: R.242 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain C: D.333, N.334 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: W.256 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshimura, M. et al., Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of the tick anticoagulant protein madanin. J.Biol.Chem. (2024)

Release Date

2024-04-10

Peptides

Protein-tyrosine sulfotransferase (Fragment): AC
Madanin Y54-peptide: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Protein-tyrosine sulfotransferase (Fragment)

Madanin Y54-peptide