SMTL ID : 6vfp.1

Crystal structure of human protocadherin 1 EC1-EC4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 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.1: 4 residues within 4Å: Chain A: E.224, N.248, D.249, S.250 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: E.224, N.248, D.249, S.250 No protein-ligand interaction detected (PLIP)

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

NAG.2: 6 residues within 4Å: Chain A: T.339, H.340, Q.341, M.344, A.345, N.346 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.339 Hydrogen bonds: A:Q.341 NAG.14: 6 residues within 4Å: Chain B: T.339, H.340, Q.341, M.344, A.345, N.346 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.339 Hydrogen bonds: B:Q.341

20 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.9, E.10, D.59, R.60, E.61, D.106 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.9, A:E.10, A:D.59, A:E.61, H2O.1 CA.4: 6 residues within 4Å: Chain A: E.122, D.182, R.183, E.184, D.218, N.219 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.122, A:D.182, A:E.184, A:D.218, H2O.1 CA.5: 8 residues within 4Å: Chain A: N.105, N.107, P.109, D.137, D.139, N.143, G.144, D.197 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.107, A:D.137, A:D.139, A:N.143, A:D.197 CA.6: 8 residues within 4Å: Chain A: N.324, N.326, A.327, P.328, D.364, D.366, N.370, D.423 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.326, A:D.364, A:D.366, A:N.370, A:D.423 CA.7: 7 residues within 4Å: Chain A: E.9, R.60, E.61, D.103, I.104, D.106, D.139 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.61, A:D.103, A:I.104, A:D.139 CA.8: 8 residues within 4Å: Chain A: E.122, R.183, E.184, D.215, T.216, D.218, N.219, D.251 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.122, A:E.184, A:D.215, A:T.216, A:D.251 CA.9: 8 residues within 4Å: Chain A: N.217, N.219, A.220, P.221, D.249, D.251, N.255, D.304 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.219, A:D.249, A:D.251, A:N.255, A:D.304 CA.10: 7 residues within 4Å: Chain A: E.234, R.290, E.291, D.322, M.323, D.325, D.366 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.291, A:D.322, A:M.323, A:D.325, A:D.366 CA.11: 6 residues within 4Å: Chain A: E.234, N.235, D.289, R.290, E.291, D.325 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.234, A:D.289, A:E.291, A:D.325, H2O.1 CA.12: 1 residues within 4Å: Chain A: D.408 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.408 CA.15: 6 residues within 4Å: Chain B: E.9, E.10, D.59, R.60, E.61, D.106 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.9, B:E.10, B:D.59, B:E.61, H2O.1 CA.16: 6 residues within 4Å: Chain B: E.122, D.182, R.183, E.184, D.218, N.219 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.122, B:D.182, B:E.184, B:D.218, H2O.1 CA.17: 8 residues within 4Å: Chain B: N.105, N.107, P.109, D.137, D.139, N.143, G.144, D.197 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.107, B:D.137, B:D.139, B:N.143, B:D.197 CA.18: 8 residues within 4Å: Chain B: N.324, N.326, A.327, P.328, D.364, D.366, N.370, D.423 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.326, B:D.364, B:D.366, B:N.370, B:D.423 CA.19: 7 residues within 4Å: Chain B: E.9, R.60, E.61, D.103, I.104, D.106, D.139 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.61, B:D.103, B:I.104, B:D.139 CA.20: 8 residues within 4Å: Chain B: E.122, R.183, E.184, D.215, T.216, D.218, N.219, D.251 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.122, B:E.184, B:D.215, B:T.216, B:D.251 CA.21: 8 residues within 4Å: Chain B: N.217, N.219, A.220, P.221, D.249, D.251, N.255, D.304 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.219, B:D.249, B:D.251, B:N.255, B:D.304 CA.22: 7 residues within 4Å: Chain B: E.234, R.290, E.291, D.322, M.323, D.325, D.366 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.291, B:D.322, B:M.323, B:D.325, B:D.366 CA.23: 6 residues within 4Å: Chain B: E.234, N.235, D.289, R.290, E.291, D.325 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.234, B:D.289, B:E.291, B:D.325, H2O.1 CA.24: 1 residues within 4Å: Chain B: D.408 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.408

Links

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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-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protocadherin-1