SMTL ID : 4zi8.1

Structure of mouse clustered PcdhgC3 EC1-3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

15 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: N.228, N.230, D.260, D.262, N.266, D.316 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.230, A:D.260, A:D.262, A:N.266, A:D.316 CA.2: 4 residues within 4Å: Chain A: E.136, D.193, E.195, D.229 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.136, A:D.193, A:D.229, H2O.8, H2O.9 CA.3: 7 residues within 4Å: Chain A: E.136, E.195, D.226, A.227, D.229, N.230, D.262 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.136, A:E.195, A:D.226, A:A.227, A:D.229, A:D.262 CA.4: 5 residues within 4Å: Chain A: E.29, E.30, D.83, E.85, D.120 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.29, A:E.30, A:D.83, A:E.85, A:D.120, H2O.7 CA.5: 7 residues within 4Å: Chain A: E.29, E.85, D.117, I.118, D.120, N.121, D.153 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.29, A:D.117, A:I.118, A:D.120, A:D.153 CA.6: 6 residues within 4Å: Chain A: N.119, N.121, D.151, D.153, N.157, D.208 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.121, A:D.151, A:D.153, A:N.157, A:D.208 CA.7: 4 residues within 4Å: Chain A: E.245, E.303 Ligands: CA.8, CA.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.245, A:E.245, A:E.303, A:E.303 CA.8: 3 residues within 4Å: Chain A: E.245, D.334 Ligands: CA.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.245, A:D.334, A:D.334 CA.9: 3 residues within 4Å: Chain A: D.301, E.303 Ligands: CA.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.301, A:D.301, A:E.303 CA.12: 6 residues within 4Å: Chain B: N.119, N.121, D.151, D.153, N.157, D.208 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.121, B:D.151, B:D.153, B:N.157, B:D.208 CA.13: 7 residues within 4Å: Chain B: E.29, E.85, D.117, I.118, D.120, N.121, D.153 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.29, B:D.117, B:I.118, B:D.120, B:D.153 CA.14: 5 residues within 4Å: Chain B: E.29, E.30, D.83, E.85, D.120 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.29, B:E.30, B:D.83, B:E.85, B:D.120, H2O.20 CA.15: 8 residues within 4Å: Chain B: E.136, E.195, D.226, A.227, D.229, N.230, D.262 Ligands: CA.16 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.136, B:D.226, B:A.227, B:D.229, B:D.262 CA.16: 5 residues within 4Å: Chain B: E.136, D.193, E.195, D.229 Ligands: CA.15 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.136, B:D.193, B:E.195, B:D.229, H2O.18, H2O.20 CA.17: 6 residues within 4Å: Chain B: N.228, N.230, D.260, D.262, N.266, D.316 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.230, B:D.260, B:D.262, B:N.266, B:D.316

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 1 residues within 4Å: Chain A: R.33 Ligand excluded by PLIP

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.11: 4 residues within 4Å: Chain A: S.275, H.276, H.325 Chain B: D.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.276 Water bridges: A:S.275, A:H.276 MPD.20: 5 residues within 4Å: Chain A: T.90, D.179 Chain B: S.275, H.276, H.325 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.325 Hydrogen bonds: A:D.179

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

NA.18: 2 residues within 4Å: Chain B: N.14, Y.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.16, B:Y.16

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

EPE.19: 3 residues within 4Å: Chain B: D.288, V.290, T.291 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.288 Salt bridges: B:D.288, B:D.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicoludis, J.M. et al., Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity. Structure (2015)

Release Date

2015-10-28

Peptides

Protein Pcdhgc3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein Pcdhgc3