SMTL ID : 6vfv.1

Crystal structure of human protocadherin 8 EC5-EC6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-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-MAN-FUC.1: 2 residues within 4Å: Chain A: N.127, T.216 No protein-ligand interaction detected (PLIP)

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

MAN.2: 4 residues within 4Å: Chain A: Q.91, Q.99, L.100, S.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.91, A:Q.91

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: N.2, N.4, A.5, D.34, D.36, N.40, G.41, D.94 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.4, A:D.34, A:D.36, A:N.40, A:D.94 CA.4: 5 residues within 4Å: Chain A: E.19, D.79, E.81, D.115, H.116 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.19, A:D.79, A:E.81, A:D.115 CA.5: 8 residues within 4Å: Chain A: E.19, Y.80, E.81, D.112, Q.113, D.115, H.116, D.153 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.19, A:E.81, A:D.112, A:Q.113, A:D.153 CA.6: 6 residues within 4Å: Chain A: N.114, H.116, D.151, D.153, N.157, D.205 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.116, A:D.151, A:D.153, A:N.157, A:D.205

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: D.115, H.116, A.117, L.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.117, A:A.117

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

CL.8: 2 residues within 4Å: Chain A: G.24, L.75 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins. Cell Rep (2020)

Release Date

2020-03-11

Peptides

Protocadherin-8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protocadherin-8