SMTL ID : 6n2e.1

Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-mer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.28, E.29, D.84, D.86, D.122, N.123 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.29, A:D.84, A:D.86, A:D.122 CA.2: 7 residues within 4Å: Chain A: E.28, D.86, D.119, R.120, D.122, N.123, D.160 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.86, A:D.86, A:D.119, A:R.120, A:D.160 CA.3: 6 residues within 4Å: Chain A: N.121, N.123, D.158, D.160, N.164, D.216 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.123, A:D.158, A:D.160, A:N.164, A:D.216 CA.4: 5 residues within 4Å: Chain A: E.138, D.237, G.238, D.240, D.290 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.138, A:D.237, A:G.238, A:D.240, A:D.290 CA.5: 5 residues within 4Å: Chain A: D.239, L.241, D.288, D.290, Q.349 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.239, A:L.241, A:D.288, A:D.288, A:D.290 CA.6: 5 residues within 4Å: Chain B: E.28, E.29, D.84, D.86, D.122 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.28, B:E.29, B:D.84, B:D.86, B:D.122, H2O.2 CA.7: 6 residues within 4Å: Chain B: E.28, D.86, D.119, R.120, D.122, D.160 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.28, B:D.86, B:D.86, B:D.119, B:R.120 CA.8: 6 residues within 4Å: Chain B: N.121, N.123, D.158, D.160, N.164, D.216 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.123, B:D.158, B:D.160, B:N.164, B:D.216 CA.9: 5 residues within 4Å: Chain B: D.239, L.241, D.288, D.290, Q.349 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.239, B:L.241, B:D.288, B:D.288, B:D.290 CA.10: 5 residues within 4Å: Chain B: E.138, D.237, G.238, D.240, D.290 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.138, B:D.237, B:G.238, B:D.240, B:D.290, H2O.2 CA.11: 6 residues within 4Å: Chain C: N.104, N.106, D.136, D.138, G.142, D.187 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.106, C:D.136, C:D.138, C:G.142, C:D.187 CA.12: 5 residues within 4Å: Chain C: E.22, D.72, E.74, D.105, N.106 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.22, C:D.72, C:E.74, C:D.105, H2O.3 CA.13: 6 residues within 4Å: Chain C: E.22, E.74, D.102, V.103, D.105, D.138 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.74, C:E.74, C:D.102, C:V.103, C:D.138 CA.14: 7 residues within 4Å: Chain C: N.4, R.5, L.6, D.37, D.39, D.41, D.87 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:R.5, C:D.37, C:D.37, C:D.39, C:D.87 CA.15: 6 residues within 4Å: Chain D: N.104, N.106, D.136, D.138, G.142, D.187 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:N.106, D:D.136, D:D.138, D:G.142, D:D.187 CA.16: 8 residues within 4Å: Chain D: E.22, E.74, D.102, V.103, D.105, N.106, D.138 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.22, D:E.74, D:V.103, D:D.105, D:D.138 CA.17: 6 residues within 4Å: Chain D: E.22, D.72, R.73, E.74, D.105 Ligands: CA.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.22, D:D.72, D:E.74, D:D.105, H2O.3 CA.18: 6 residues within 4Å: Chain D: N.4, R.5, D.37, D.39, D.41, D.87 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:R.5, D:D.37, D:D.37, D:D.39, D:D.41

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

2019-11-13

Peptides

Protocadherin-15: AB
Cadherin-23: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Protocadherin-15

Cadherin-23

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