SMTL ID : 5d7f.1

X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

hetero-2-1-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.19, A:E.22, A:D.24, A:K.27, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.62, A:E.68, A:E.73, A:E.73, H2O.2 CA.8: 5 residues within 4Å: Chain B: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.19, B:E.22, B:D.24, B:K.27, H2O.5 CA.9: 5 residues within 4Å: Chain B: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.62, B:E.68, B:E.73, B:E.73, H2O.6

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: K.49, E.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.49 GOL.4: 3 residues within 4Å: Chain A: M.80, T.83, A.84 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.72, B:Q.72 Hydrogen bonds: A:A.84 GOL.5: 4 residues within 4Å: Chain A: R.21, E.22, G.23 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain A: G.23, K.29 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.23 Water bridges: A:D.24 GOL.7: 5 residues within 4Å: Chain A: K.30, S.31, K.34, Q.51, V.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.51 Water bridges: A:K.34 GOL.10: 5 residues within 4Å: Chain B: K.30, S.31, K.34, Q.51, V.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.51, B:Q.51 Water bridges: B:S.31, B:K.34, B:K.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jensen, J.L. et al., X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide. To Be Published

Release Date

2016-08-17

Peptides

Protein S100-B: AB
Advanced glycosylation end product-specific receptor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
P

Protein S100-B

Advanced glycosylation end product-specific receptor

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