SMTL ID : 6mga.2 (1 other biounit)

Crystal Structure of Human Protocadherin-1 EC1-4 with glycosylation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.224, N.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.224 NAG.12: 2 residues within 4Å: Chain B: E.224, N.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.224

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

MAN.2: 4 residues within 4Å: Chain A: S.430 Chain B: S.113, V.115, T.117 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.113, B:S.113, B:T.117 MAN.13: 4 residues within 4Å: Chain A: S.113, V.115, T.117 Chain B: S.430 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.113, A:S.113

18 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.9, E.10, D.59, E.61, D.106 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.10, A:D.59, A:E.61, A:D.106 CA.4: 7 residues within 4Å: Chain A: E.9, E.61, D.103, I.104, D.106, N.107, 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.5: 6 residues within 4Å: Chain A: N.105, N.107, D.137, D.139, N.143, 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: 4 residues within 4Å: Chain A: E.122, D.182, E.184, D.218 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.122, A:D.182, A:E.184, A:D.218 CA.7: 6 residues within 4Å: Chain A: E.122, E.184, D.215, T.216, D.218, 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.8: 6 residues within 4Å: Chain A: N.217, N.219, 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.9: 4 residues within 4Å: Chain A: E.234, D.289, E.291, D.325 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.234, A:D.289, A:E.291, A:D.325 CA.10: 6 residues within 4Å: Chain A: E.234, E.291, D.322, M.323, D.325, D.366 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.234, A:D.322, A:M.323, A:D.325, A:D.366 CA.11: 6 residues within 4Å: Chain A: N.324, N.326, 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.14: 5 residues within 4Å: Chain B: E.9, E.10, D.59, E.61, D.106 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.10, B:D.59, B:E.61, B:D.106 CA.15: 7 residues within 4Å: Chain B: E.9, E.61, D.103, I.104, D.106, N.107, 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.16: 6 residues within 4Å: Chain B: N.105, N.107, D.137, D.139, N.143, 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.17: 4 residues within 4Å: Chain B: E.122, D.182, E.184, D.218 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.122, B:D.182, B:E.184, B:D.218 CA.18: 6 residues within 4Å: Chain B: E.122, E.184, D.215, T.216, D.218, 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.19: 6 residues within 4Å: Chain B: N.217, N.219, 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.20: 4 residues within 4Å: Chain B: E.234, D.289, E.291, D.325 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.234, B:D.289, B:E.291, B:D.325 CA.21: 6 residues within 4Å: Chain B: E.234, E.291, D.322, M.323, D.325, D.366 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.234, B:D.322, B:M.323, B:D.325, B:D.366 CA.22: 6 residues within 4Å: Chain B: N.324, N.326, 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

Links

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Citation

Modak, D. et al., Identification of an adhesive interface for the non-clustered delta 1 protocadherin-1 involved in respiratory diseases. Commun Biol (2019)

Release Date

2019-09-18

Peptides

Protocadherin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protocadherin-1

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