SMTL ID : 7wbo.1

Crystal structure of Sarcoplasmic Calcium-Binding Protein from Scylla paramamosain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: D.155, K.158, K.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.159 EDO.2: 3 residues within 4Å: Chain A: W.8, K.90, P.179 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.90 EDO.3: 5 residues within 4Å: Chain A: I.134, S.135, R.136, S.137, A.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.135 EDO.4: 5 residues within 4Å: Chain A: R.17, Y.18, D.21, I.22, N.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17 Water bridges: A:Y.18 EDO.5: 4 residues within 4Å: Chain A: Y.6, E.181, K.182, Y.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.181 EDO.6: 6 residues within 4Å: Chain A: K.13, V.16, R.17, D.21, G.26, V.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17, A:D.21 EDO.7: 4 residues within 4Å: Chain A: D.83, K.86, Q.87, K.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.87 Water bridges: A:D.9, A:K.90, A:K.90

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: D.21, D.23, N.25, Y.27, D.32 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.21, A:Y.27, A:D.32, A:D.32, H2O.2 CA.9: 5 residues within 4Å: Chain A: D.73, N.75, D.77, Q.79, E.84 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.73, A:D.77, A:Q.79, A:E.84, H2O.5 CA.10: 5 residues within 4Å: Chain A: D.117, N.119, D.121, L.123, E.128 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.117, A:D.121, A:L.123, A:E.128, H2O.7 CA.11: 4 residues within 4Å: Chain A: G.125, V.126, D.127, E.128 No protein-ligand interaction detected (PLIP)

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

NA.12: 5 residues within 4Å: Chain A: E.67, L.71, P.102, P.103, C.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.104 Water bridges: A:E.67, A:E.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Crystal Structure Analysis of Sarcoplasmic-Calcium-Binding Protein: An Allergen in Scylla paramamosain. J.Agric.Food Chem. (2023)

Release Date

2022-12-21

Peptides

Sarcoplasmic calcium-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sarcoplasmic calcium-binding protein