SMTL ID : 5v5x.1

Protocadherin gammaB7 EC3-6 cis-dimer structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain B: S.304, A.305, N.306 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain B: G.178, N.180 Ligands: MAN.19 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 4 residues within 4Å: Chain C: N.180 Chain D: P.20, G.21, T.22 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:T.22

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.4: 3 residues within 4Å: Chain D: S.304, A.305, N.306 No protein-ligand interaction detected (PLIP)

36 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: E.16, D.69, E.71, D.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.16, A:D.69, A:E.71, A:D.103 CA.6: 6 residues within 4Å: Chain A: E.16, E.71, D.100, E.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.16, A:E.71, A:D.100, A:E.101, A:D.103 CA.7: 6 residues within 4Å: Chain A: N.102, N.104, D.134, D.136, N.140, D.187 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.104, A:D.134, A:D.136, A:N.140, A:D.187 CA.8: 5 residues within 4Å: Chain A: E.119, D.172, E.174, D.208, N.209 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.119, A:D.172, A:E.174, A:D.208 CA.9: 6 residues within 4Å: Chain A: E.119, E.174, D.205, V.206, D.208, D.241 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.119, A:E.174, A:V.206, A:D.208, A:D.241 CA.10: 6 residues within 4Å: Chain A: N.207, N.209, D.239, D.241, N.245, D.297 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.209, A:D.239, A:D.241, A:N.245, A:D.297 CA.11: 5 residues within 4Å: Chain A: E.224, N.225, D.282, E.284, D.318 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.224, A:D.282, A:E.284, A:D.318 CA.12: 6 residues within 4Å: Chain A: E.224, E.284, D.315, R.316, D.318, D.358 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.224, A:E.284, A:R.316, A:D.318, A:D.358 CA.13: 6 residues within 4Å: Chain A: N.317, N.319, D.356, D.358, N.362, D.409 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.319, A:D.356, A:D.356, A:D.358, A:N.362 CA.22: 4 residues within 4Å: Chain B: E.16, D.69, E.71, D.103 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.16, B:D.69, B:E.71, B:D.103 CA.23: 6 residues within 4Å: Chain B: E.16, E.71, D.100, E.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.16, B:E.71, B:D.100, B:E.101, B:D.103 CA.24: 6 residues within 4Å: Chain B: N.102, N.104, D.134, D.136, N.140, D.187 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.104, B:D.134, B:D.136, B:N.140, B:D.187 CA.25: 4 residues within 4Å: Chain B: E.119, D.172, E.174, D.208 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.119, B:D.172, B:E.174, B:D.208 CA.26: 6 residues within 4Å: Chain B: E.119, E.174, D.205, V.206, D.208, D.241 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.119, B:E.174, B:V.206, B:D.208, B:D.241 CA.27: 6 residues within 4Å: Chain B: N.207, N.209, D.239, D.241, N.245, D.297 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.239, B:D.239, B:D.241, B:N.245, B:D.297 CA.28: 5 residues within 4Å: Chain B: E.224, N.225, D.282, E.284, D.318 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.224, B:D.282, B:E.284, B:D.318 CA.29: 6 residues within 4Å: Chain B: E.224, E.284, D.315, R.316, D.318, D.358 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.224, B:E.284, B:D.315, B:R.316, B:D.358 CA.30: 6 residues within 4Å: Chain B: N.317, N.319, D.356, D.358, N.362, D.409 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.319, B:D.356, B:D.358, B:N.362, B:D.409 CA.37: 4 residues within 4Å: Chain C: E.16, D.69, E.71, D.103 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.16, C:D.69, C:E.71, C:D.103 CA.38: 6 residues within 4Å: Chain C: E.16, E.71, D.100, E.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.71, C:D.100, C:E.101, C:D.103, C:D.136 CA.39: 6 residues within 4Å: Chain C: N.102, N.104, D.134, D.136, N.140, D.187 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.134, C:D.134, C:D.136, C:N.140, C:D.187 CA.40: 5 residues within 4Å: Chain C: E.119, D.172, E.174, D.208, N.209 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.172, C:E.174, C:D.208 CA.41: 6 residues within 4Å: Chain C: E.119, E.174, D.205, V.206, D.208, D.241 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.174, C:D.205, C:V.206, C:D.208, C:D.241 CA.42: 6 residues within 4Å: Chain C: N.207, N.209, D.239, D.241, N.245, D.297 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.209, C:D.239, C:D.239, C:D.241, C:N.245 CA.43: 5 residues within 4Å: Chain C: E.224, D.282, E.284, D.318 Ligands: CA.44 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.224, C:D.282, C:E.284, C:D.318 CA.44: 7 residues within 4Å: Chain C: E.224, E.284, D.315, R.316, D.318, D.358 Ligands: CA.43 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.224, C:E.284, C:R.316, C:D.318, C:D.358 CA.45: 6 residues within 4Å: Chain C: N.317, N.319, D.356, D.358, N.362, D.409 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.319, C:D.356, C:D.358, C:N.362, C:D.409 CA.53: 4 residues within 4Å: Chain D: E.16, D.69, E.71, D.103 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.16, D:D.69, D:E.71, D:D.103 CA.54: 6 residues within 4Å: Chain D: E.16, E.71, D.100, E.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.16, D:E.71, D:D.100, D:E.101, D:D.103 CA.55: 6 residues within 4Å: Chain D: N.102, N.104, D.134, D.136, N.140, D.187 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:N.104, D:D.134, D:D.136, D:N.140, D:D.187 CA.56: 4 residues within 4Å: Chain D: E.119, D.172, E.174, D.208 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.119, D:D.172, D:E.174, D:D.208 CA.57: 6 residues within 4Å: Chain D: E.119, E.174, D.205, V.206, D.208, D.241 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.119, D:D.205, D:V.206, D:D.208, D:D.241 CA.58: 6 residues within 4Å: Chain D: N.207, N.209, D.239, D.241, N.245, D.297 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.239, D:D.239, D:D.241, D:N.245, D:D.297 CA.59: 5 residues within 4Å: Chain D: E.224, N.225, D.282, E.284, D.318 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.224, D:D.282, D:E.284, D:D.318 CA.60: 6 residues within 4Å: Chain D: E.224, E.284, D.315, R.316, D.318, D.358 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.224, D:E.284, D:D.315, D:R.316, D:D.358 CA.61: 6 residues within 4Å: Chain D: N.317, N.319, D.356, D.358, N.362, D.409 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:N.319, D:D.356, D:D.358, D:N.362, D:D.409

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

MAN.14: 2 residues within 4Å: Chain A: S.194 Ligands: MAN.15 No protein-ligand interaction detected (PLIP) MAN.15: 3 residues within 4Å: Chain A: S.194, S.196 Ligands: MAN.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.194 MAN.16: 4 residues within 4Å: Chain A: S.231, T.233, Q.234, V.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.234 MAN.17: 5 residues within 4Å: Chain A: R.408, P.414, S.416, T.418 Ligands: MAN.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.408 MAN.18: 3 residues within 4Å: Chain A: T.418, A.419 Ligands: MAN.17 No protein-ligand interaction detected (PLIP) MAN.19: 6 residues within 4Å: Chain A: G.21, T.23, R.26, T.59, D.61 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.21, A:R.26 MAN.31: 3 residues within 4Å: Chain B: P.192, S.194 Ligands: MAN.32 No protein-ligand interaction detected (PLIP) MAN.32: 2 residues within 4Å: Chain B: S.196 Ligands: MAN.31 No protein-ligand interaction detected (PLIP) MAN.33: 4 residues within 4Å: Chain B: S.231, T.233, Q.234, V.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.234 MAN.34: 4 residues within 4Å: Chain B: R.408, S.416, T.418 Ligands: MAN.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.408, B:R.408 MAN.35: 3 residues within 4Å: Chain B: L.404, T.418 Ligands: MAN.34 No protein-ligand interaction detected (PLIP) MAN.36: 5 residues within 4Å: Chain B: G.21, T.23, R.26, D.61 Ligands: NAG.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.21, B:R.26, B:D.61 MAN.46: 4 residues within 4Å: Chain C: T.186, P.192, S.194 Ligands: MAN.47 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.186 MAN.47: 3 residues within 4Å: Chain C: T.184, S.196 Ligands: MAN.46 No protein-ligand interaction detected (PLIP) MAN.48: 4 residues within 4Å: Chain C: S.231, T.233, Q.234, V.274 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.234 MAN.49: 3 residues within 4Å: Chain C: R.408, P.414, S.416 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.408 MAN.50: 3 residues within 4Å: Chain C: D.331, T.418, A.419 No protein-ligand interaction detected (PLIP) MAN.51: 6 residues within 4Å: Chain C: G.21, T.23, R.26, D.61, V.63 Ligands: NAG.68 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.21, C:R.26, C:R.26 MAN.62: 3 residues within 4Å: Chain D: T.186, P.192, S.194 No protein-ligand interaction detected (PLIP) MAN.63: 1 residues within 4Å: Chain D: S.196 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.196 MAN.64: 4 residues within 4Å: Chain D: S.231, T.233, Q.234, V.274 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.234 MAN.65: 5 residues within 4Å: Chain D: R.408, P.414, S.416, T.418 Ligands: MAN.66 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.408 MAN.66: 2 residues within 4Å: Chain D: T.418 Ligands: MAN.65 No protein-ligand interaction detected (PLIP) MAN.67: 4 residues within 4Å: Chain D: G.21, T.23, R.26, D.61 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.21, D:R.26

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

NAG.20: 3 residues within 4Å: Chain A: S.304, A.305, N.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.306 NAG.21: 2 residues within 4Å: Chain A: N.180 Ligands: MAN.36 No protein-ligand interaction detected (PLIP) NAG.52: 3 residues within 4Å: Chain C: I.253, S.304, N.306 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.306 NAG.68: 4 residues within 4Å: Chain D: G.178, Y.179, N.180 Ligands: MAN.51 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodman, K.M. et al., Protocadherin cis-dimer architecture and recognition unit diversity. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-11-01

Peptides

MCG133388, isoform CRA_y: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

MCG133388, isoform CRA_y