SMTL ID : 5szo.1

Protocadherin Gamma B7 extracellular cadherin domains 1-4 P41212 crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.61 Å

Oligo State

homo-dimer

Ligands

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

NAG-FUC.1: 2 residues within 4Å: Chain B: N.387, T.407 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.407

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

MAN.2: 4 residues within 4Å: Chain A: V.185, P.191, T.193 Ligands: MAN.3 No protein-ligand interaction detected (PLIP) MAN.3: 2 residues within 4Å: Chain A: T.195 Ligands: MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.197 MAN.4: 3 residues within 4Å: Chain A: T.393, P.399, S.401 No protein-ligand interaction detected (PLIP) MAN.5: 2 residues within 4Å: Chain A: T.389, S.403 No protein-ligand interaction detected (PLIP) MAN.15: 4 residues within 4Å: Chain B: V.185, P.191, T.193 Ligands: MAN.16 No protein-ligand interaction detected (PLIP) MAN.16: 2 residues within 4Å: Chain B: T.195 Ligands: MAN.15 No protein-ligand interaction detected (PLIP) MAN.17: 4 residues within 4Å: Chain B: T.393, P.399, S.401 Ligands: MAN.18 No protein-ligand interaction detected (PLIP) MAN.18: 3 residues within 4Å: Chain B: T.391, S.403 Ligands: MAN.17 No protein-ligand interaction detected (PLIP)

18 x CA: CALCIUM ION(Non-covalent)

CA.6: 7 residues within 4Å: Chain A: E.9, E.10, D.61, E.63, D.98, H.99 Ligands: CA.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.61, A:D.98 CA.7: 8 residues within 4Å: Chain A: E.9, E.63, D.95, V.96, D.98, H.99, D.131 Ligands: CA.6 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.8: 6 residues within 4Å: Chain A: N.97, H.99, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.99, A:D.129, A:D.131, A:N.135, A:D.186 CA.9: 6 residues within 4Å: Chain A: E.114, D.171, E.173, D.207, N.208 Ligands: CA.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.114, A:D.171, A:E.173, A:D.207 CA.10: 7 residues within 4Å: Chain A: E.114, E.173, D.204, A.205, D.207, D.240 Ligands: CA.9 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.11: 6 residues within 4Å: Chain A: N.206, N.208, D.238, D.240, N.244, D.291 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.208, A:D.238, A:D.240, A:N.244, A:D.291 CA.12: 6 residues within 4Å: Chain A: E.223, D.276, E.278, D.310, N.311 Ligands: CA.13 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:E.278, A:D.310, A:D.310 CA.13: 8 residues within 4Å: Chain A: E.223, E.278, D.307, E.308, D.310, N.311, D.343 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.223, A:E.278, A:D.307, A:D.310, A:D.343 CA.14: 6 residues within 4Å: Chain A: N.309, N.311, D.341, D.343, N.347, D.394 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.311, A:D.341, A:D.341, A:D.343, A:N.347 CA.19: 7 residues within 4Å: Chain B: E.9, E.10, D.61, E.63, D.98, H.99 Ligands: CA.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.9, B:D.61, B:E.63, B:D.98 CA.20: 8 residues within 4Å: Chain B: E.9, E.63, D.95, V.96, D.98, H.99, D.131 Ligands: CA.19 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.63, B:D.95, B:V.96, B:D.131 CA.21: 7 residues within 4Å: Chain B: N.97, H.99, P.101, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.129, B:D.129, B:D.131, B:N.135, B:D.186 CA.22: 6 residues within 4Å: Chain B: E.114, D.171, E.173, D.207, N.208 Ligands: CA.23 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.114, B:D.171, B:D.207 CA.23: 7 residues within 4Å: Chain B: E.114, E.173, D.204, A.205, D.207, D.240 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.114, B:E.173, B:D.204, B:D.207, B:D.240 CA.24: 6 residues within 4Å: Chain B: N.206, N.208, D.238, D.240, N.244, D.291 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.208, B:D.238, B:D.240, B:N.244, B:D.291 CA.25: 6 residues within 4Å: Chain B: E.223, D.276, E.278, D.310, N.311 Ligands: CA.26 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.223, B:D.276, B:D.310 CA.26: 8 residues within 4Å: Chain B: E.223, E.278, D.307, E.308, D.310, N.311, D.343 Ligands: CA.25 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.223, B:E.278, B:D.307, B:D.310 CA.27: 6 residues within 4Å: Chain B: N.309, N.311, D.341, D.343, N.347, D.394 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.311, B:D.341, B:D.343, B:N.347, B:D.394

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 B7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protocadherin Gamma B7

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