SMTL ID : 5szp.1

Protocadherin Gamma B7 extracellular cadherin domains 1-4 P21 crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.9, E.10, D.61, E.63, D.98, H.99 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.9, A:D.61, A:E.63, A:D.98 CA.2: 7 residues within 4Å: Chain A: E.9, E.63, D.95, V.96, D.98, H.99, D.131 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.3: 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.4: 6 residues within 4Å: Chain A: E.114, D.171, E.173, D.207, N.208 Ligands: CA.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.114, A:D.171, A:E.173, A:D.207 CA.5: 8 residues within 4Å: Chain A: E.114, R.172, E.173, D.204, A.205, D.207, D.240 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.114, A:E.173, A:D.204, A:A.205, A:D.240 CA.6: 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.7: 5 residues within 4Å: Chain A: E.223, D.276, E.278, D.310 Ligands: CA.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.223, A:D.276, A:E.278, A:D.310, A:D.310 CA.8: 7 residues within 4Å: Chain A: E.223, E.278, D.307, E.308, D.310, D.343 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.223, A:E.278, A:E.308, A:D.310, A:D.343 CA.9: 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.16: 6 residues within 4Å: Chain B: E.9, E.10, D.61, E.63, D.98 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.9, B:E.10, B:D.61, B:E.63 CA.17: 7 residues within 4Å: Chain B: E.9, E.63, D.95, V.96, D.98, D.131 Ligands: CA.16 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:D.95, B:V.96, B:D.98, B:D.131 CA.18: 6 residues within 4Å: Chain B: N.97, H.99, D.129, D.131, N.135, D.186 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.99, B:D.129, B:D.131, B:N.135, B:D.186 CA.19: 6 residues within 4Å: Chain B: E.114, D.171, E.173, D.207, N.208 Ligands: CA.20 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.114, B:D.171, B:E.173, B:D.207, B:D.207 CA.20: 7 residues within 4Å: Chain B: E.114, E.173, D.204, A.205, D.207, D.240 Ligands: CA.19 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.114, B:E.173, B:D.204, B:A.205, B:D.240 CA.21: 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:D.238, B:D.238, B:D.240, B:N.244, B:D.291 CA.22: 6 residues within 4Å: Chain B: E.223, D.276, E.278, D.310, N.311 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.223, B:D.276, B:E.278, B:D.310, B:D.310 CA.23: 7 residues within 4Å: Chain B: E.223, E.278, D.307, E.308, D.310, D.343 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.223, B:E.278, B:D.307, B:E.308, B:D.310 CA.24: 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

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

MAN.10: 5 residues within 4Å: Chain A: Q.141, V.185, P.191, T.193 Ligands: MAN.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.141, A:Q.141, A:P.191 MAN.11: 4 residues within 4Å: Chain A: M.181, T.193, T.195 Ligands: MAN.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.193, A:Q.197 MAN.12: 2 residues within 4Å: Chain A: P.399, S.401 No protein-ligand interaction detected (PLIP) MAN.13: 2 residues within 4Å: Chain A: T.230, D.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.268 MAN.25: 4 residues within 4Å: Chain B: V.185, P.191, T.193 Ligands: MAN.26 No protein-ligand interaction detected (PLIP) MAN.26: 3 residues within 4Å: Chain B: T.193, T.195 Ligands: MAN.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.193 MAN.27: 3 residues within 4Å: Chain B: T.230, D.268, V.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.268

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

NAG.14: 1 residues within 4Å: Chain A: N.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.387

1 x TMO: trimethylamine oxide(Non-covalent)

TMO.15: 4 residues within 4Å: Chain A: R.121, E.163 Chain B: D.215, Q.298 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:D.215, A:E.163

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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