SMTL ID : 7f9g.1

Thrombocorticin in complex with Ca2+ and fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-dimer

Ligands

2 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.1: 11 residues within 4Å: Chain A: Q.34, S.35, S.36, G.61, D.117, D.124, D.126, D.129 Chain B: G.140 Ligands: CA.2, CA.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.36, A:D.117, A:D.124, B:G.140 Water bridges: A:R.37, A:R.37, A:R.37 FUC.4: 11 residues within 4Å: Chain A: G.140 Chain B: Q.34, S.35, S.36, R.37, G.62, D.117, D.124, D.129 Ligands: CA.5, CA.6 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.36, B:R.37, B:D.117, B:D.117, A:G.140 Water bridges: B:R.37, B:D.124 Salt bridges: B:R.37

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: Q.34, D.126, N.128, D.129 Chain B: G.140 Ligands: FUC.1, CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Q.34, A:D.126, A:D.129 CA.3: 6 residues within 4Å: Chain A: N.116, D.124, D.126, D.129 Ligands: FUC.1, CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.124, A:D.126, A:D.129, A:D.129, H2O.3 CA.5: 5 residues within 4Å: Chain A: G.140 Chain B: Q.34, N.128, D.129 Ligands: FUC.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Q.34, B:D.129 CA.6: 4 residues within 4Å: Chain B: N.116, D.124, D.129 Ligands: FUC.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.124, B:D.129, B:D.129, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watari, H. et al., A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation. Nat Commun (2022)

Release Date

2022-07-06

Peptides

Thrombocorticin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thrombocorticin

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