SMTL ID : 4zml.1

Crystal structure of human P-cadherin (ss-dimer)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.11, E.69, D.100, Q.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:D.100, A:Q.101, A:D.103, A:D.136 CA.2: 4 residues within 4Å: Chain A: E.11, D.67, E.69, D.103 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.11, A:D.67, A:E.69, A:D.103, H2O.1, H2O.5 CA.3: 6 residues within 4Å: Chain A: N.102, H.104, D.134, D.136, N.143, D.195 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.104, A:D.134, A:D.136, A:N.143, A:D.195 CA.4: 3 residues within 4Å: Chain A: E.70 Chain B: E.70 Ligands: CA.13 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.70, H2O.6, H2O.6, H2O.13, H2O.13 CA.5: 1 residues within 4Å: Chain A: E.182 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.182, H2O.5 CA.10: 6 residues within 4Å: Chain B: E.11, E.69, D.100, Q.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:D.100, B:Q.101, B:D.103, B:D.136 CA.11: 4 residues within 4Å: Chain B: E.11, D.67, E.69, D.103 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.11, B:D.67, B:E.69, B:D.103, H2O.8, H2O.13 CA.12: 6 residues within 4Å: Chain B: N.102, H.104, D.134, D.136, N.143, D.195 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.104, B:D.134, B:D.136, B:N.143, B:D.195 CA.13: 3 residues within 4Å: Chain A: E.70 Chain B: E.70 Ligands: CA.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.70, H2O.6, H2O.6, H2O.13, H2O.13 CA.14: 1 residues within 4Å: Chain B: E.182 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.182, H2O.12

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

CL.6: 2 residues within 4Å: Chain A: T.99, D.100 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: E.54, K.55, E.56, T.57 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: T.99, D.100 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: E.54, K.55, E.56, T.57 Ligand excluded by PLIP

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.8: 7 residues within 4Å: Chain A: F.17, K.64, P.65 Chain B: D.67, E.69, E.70, E.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.64 P6G.17: 7 residues within 4Å: Chain A: D.67, E.69, E.70, E.135 Chain B: F.17, K.64, P.65 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.64 Water bridges: A:D.67

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 4 residues within 4Å: Chain A: I.7, Q.19, R.20, L.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.19 Water bridges: A:S.8 PG4.18: 4 residues within 4Å: Chain B: I.7, Q.19, R.20, L.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.19 Water bridges: B:S.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kudo, S. et al., Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism. Structure (2016)

Release Date

2016-09-07

Peptides

Cadherin-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cadherin-3

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