SMTL ID : 6eet.1

Crystal structure of mouse Protocadherin-15 EC9-MAD12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.23 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.257, Y.310 No protein-ligand interaction detected (PLIP)

3 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.3: 5 residues within 4Å: Chain A: R.48, V.89, V.97, S.99 Ligands: MAN.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.48 MAN.4: 5 residues within 4Å: Chain A: R.11, I.12, Q.53, V.87, T.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.11, A:R.11, A:Q.53, A:Q.53 MAN.6: 6 residues within 4Å: Chain A: D.50, V.52, Q.53, V.87, S.101 Ligands: MAN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.48, A:Q.53, A:S.99

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 4 residues within 4Å: Chain A: E.280, T.281, Y.282, T.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.281, A:Y.282, A:T.283 Salt bridges: A:E.280, A:E.280

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: E.129, E.180, D.218, E.219, D.221, D.254 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.180, A:D.218, A:E.219, A:D.221, A:D.254 CA.8: 6 residues within 4Å: Chain A: N.220, H.222, D.252, D.254, Y.258, D.308 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.222, A:D.252, A:D.254, A:Y.258, A:D.308 CA.9: 4 residues within 4Å: Chain A: E.129, D.178, E.180, D.221 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.129, A:D.178, A:E.180, A:D.221 CA.10: 6 residues within 4Å: Chain A: N.2, Y.4, D.34, D.36, A.42, D.92 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.4, A:D.34, A:D.36, A:A.42, A:D.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choudhary, D. et al., Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2019-08-21

Peptides

Protocadherin-15: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protocadherin-15