SMTL ID : 5t9t.1

Protocadherin Gamma B2 extracellular cadherin domains 1-5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-FUC.1: 2 residues within 4Å: Chain B: E.387, N.389 No protein-ligand interaction detected (PLIP)

26 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.9, E.10, D.61, E.63, D.98 Ligands: CA.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.9, A:D.61, A:E.63, A:D.98 CA.3: 7 residues within 4Å: Chain A: E.9, E.63, D.95, V.96, D.98, D.131 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.63, A:D.95, A:V.96, A:D.131 CA.4: 6 residues within 4Å: Chain A: N.97, N.99, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.129, A:D.129, A:D.131, A:N.135, A:D.186 CA.5: 5 residues within 4Å: Chain A: E.114, D.171, E.173, D.207 Ligands: CA.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.114, A:D.171, A:E.173, A:D.207 CA.6: 7 residues within 4Å: Chain A: E.114, E.173, D.204, I.205, D.207, D.240 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.114, A:E.173, A:D.204, A:D.207, A:D.240 CA.7: 6 residues within 4Å: Chain A: N.206, N.208, D.238, D.240, N.244, D.293 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.208, A:D.238, A:D.240, A:N.244, A:D.293 CA.8: 4 residues within 4Å: Chain A: E.223, D.278, E.280, D.312 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.278, A:E.280, A:D.312 CA.9: 6 residues within 4Å: Chain A: E.223, E.280, D.309, E.310, D.312, D.345 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.223, A:D.309, A:E.310, A:D.312, A:D.345 CA.10: 6 residues within 4Å: Chain A: N.311, C.313, D.343, D.345, N.349, D.396 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.313, A:D.343, A:D.343, A:D.345, A:N.349 CA.11: 5 residues within 4Å: Chain A: E.328, D.381, E.383, D.417 Ligands: CA.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.328, A:D.381, A:E.383, A:D.417 CA.12: 7 residues within 4Å: Chain A: E.328, E.383, D.414, V.415, D.417, D.450 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.328, A:D.414, A:V.415, A:D.417, A:D.450 CA.13: 6 residues within 4Å: Chain A: N.416, N.418, D.448, D.450, N.454, D.506 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.418, A:D.448, A:D.450, A:N.454, A:D.506 CA.21: 7 residues within 4Å: Chain B: E.9, E.10, D.61, E.63, D.98, N.99 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:D.61, B:E.63, B:D.98, B:D.98 CA.22: 7 residues within 4Å: Chain B: E.9, E.63, D.95, V.96, D.98, D.131 Ligands: CA.21 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.63, B:D.95, B:D.98, B:D.131 CA.23: 6 residues within 4Å: Chain B: N.97, N.99, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.99, B:D.129, B:D.131, B:N.135, B:D.186 CA.24: 4 residues within 4Å: Chain B: E.114, D.171, E.173, D.207 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.114, B:D.171, B:E.173, B:D.207 CA.25: 6 residues within 4Å: Chain B: E.114, E.173, D.204, I.205, D.207, D.240 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.114, B:D.204, B:I.205, B:D.207, B:D.240 CA.26: 6 residues within 4Å: Chain B: N.206, N.208, D.238, D.240, N.244, D.293 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.208, B:D.238, B:D.240, B:N.244, B:D.293 CA.27: 5 residues within 4Å: Chain B: E.223, D.278, E.280, D.312 Ligands: CA.28 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.223, B:D.278, B:E.280, B:D.312, B:D.312 CA.28: 7 residues within 4Å: Chain B: E.223, E.280, D.309, E.310, D.312, D.345 Ligands: CA.27 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.223, B:E.280, B:D.309, B:E.310, B:D.345 CA.29: 6 residues within 4Å: Chain B: N.311, C.313, D.343, D.345, N.349, D.396 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.313, B:D.343, B:D.345, B:N.349, B:D.396 CA.30: 5 residues within 4Å: Chain B: E.328, D.381, E.383, D.417, N.418 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.381, B:E.383, B:D.417 CA.31: 7 residues within 4Å: Chain B: E.328, E.383, D.414, V.415, D.417, N.418, D.450 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.328, B:E.383, B:D.414, B:V.415, B:D.450 CA.32: 6 residues within 4Å: Chain B: N.416, N.418, D.448, D.450, N.454, D.506 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.418, B:D.448, B:D.450, B:N.454, B:D.506 CA.33: 7 residues within 4Å: Chain B: E.433, E.493, D.524, R.525, N.526, D.527 Ligands: CA.34 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.493, B:E.493, B:R.525, B:D.527 CA.34: 5 residues within 4Å: Chain B: E.433, D.491, E.493, D.527 Ligands: CA.33 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.491, B:E.493, B:D.527, B:D.527

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

MAN.14: 2 residues within 4Å: Chain A: Y.141, S.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.141 MAN.15: 2 residues within 4Å: Chain A: S.230, Q.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.233, A:Q.233 MAN.17: 4 residues within 4Å: Chain A: S.440, A.442, Q.443, V.483 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.442 MAN.19: 4 residues within 4Å: Chain A: V.181, T.195, T.196, Q.197 No protein-ligand interaction detected (PLIP) MAN.20: 3 residues within 4Å: Chain A: V.393, S.403, N.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.405 MAN.35: 3 residues within 4Å: Chain B: V.185, P.191, S.193 No protein-ligand interaction detected (PLIP) MAN.36: 3 residues within 4Å: Chain B: T.195, T.196, Q.197 No protein-ligand interaction detected (PLIP) MAN.37: 4 residues within 4Å: Chain B: S.230, L.232, Q.233, E.270 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.232, B:E.270 MAN.38: 2 residues within 4Å: Chain B: P.401, S.403 No protein-ligand interaction detected (PLIP) MAN.39: 4 residues within 4Å: Chain B: S.440, A.442, Q.443, V.483 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.442 MAN.40: 5 residues within 4Å: Chain B: Q.443, V.444, S.445, A.446, Y.459 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.443, B:A.446, B:Y.459

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

NAG.16: 2 residues within 4Å: Chain A: E.387, N.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.387, A:N.389 NAG.18: 3 residues within 4Å: Chain A: I.462, S.513, N.515 No protein-ligand interaction detected (PLIP) NAG.41: 4 residues within 4Å: Chain B: I.462, Q.503, S.513, N.515 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.515

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodman, K.M. et al., gamma-Protocadherin structural diversity and functional implications. Elife (2016)

Release Date

2016-10-19

Peptides

Protocadherin gamma B2-alpha C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protocadherin gamma B2-alpha C