SMTL ID : 4zmw.1

Crystal structure of human P-cadherin (enc-X-dimer)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.12, E.70, D.101, Q.102, D.104, D.137 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.12, A:E.70, A:D.101, A:Q.102, A:D.137 CA.2: 6 residues within 4Å: Chain A: N.103, H.105, D.135, D.137, N.144, D.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.105, A:D.135, A:D.137, A:N.144, A:D.196 CA.6: 6 residues within 4Å: Chain B: E.12, E.70, D.101, Q.102, D.104, D.137 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.12, B:E.70, B:E.70, B:D.101, B:D.137 CA.7: 6 residues within 4Å: Chain B: N.103, H.105, D.135, D.137, N.144, D.196 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.105, B:D.135, B:D.137, B:N.144, B:D.196

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: D.68, E.70, H.105, E.136 Ligands: SO4.4, NI.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.105 SO4.4: 5 residues within 4Å: Chain A: D.68, D.104, H.105 Ligands: SO4.3, NI.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.105 SO4.8: 9 residues within 4Å: Chain A: R.69, E.136, D.137, D.138, I.140 Chain B: Q.111, T.113, F.114, R.115 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.138, B:Q.111, B:Q.111, B:R.115, B:R.115 Water bridges: A:R.69 Salt bridges: A:R.69 SO4.9: 1 residues within 4Å: Chain B: R.21 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.21 SO4.10: 4 residues within 4Å: Chain B: T.33, S.83, N.85, A.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.33, B:S.83, B:N.85, B:N.85 SO4.11: 5 residues within 4Å: Chain B: D.68, D.104, H.105 Ligands: SO4.12, NI.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.104 Salt bridges: B:H.105 SO4.12: 7 residues within 4Å: Chain B: D.68, E.70, E.71, H.105, E.136 Ligands: SO4.11, NI.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.68 Salt bridges: B:H.105

2 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 3 residues within 4Å: Chain A: H.105 Ligands: SO4.3, SO4.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.105, H2O.1 NI.13: 4 residues within 4Å: Chain B: H.105, E.136 Ligands: SO4.11, SO4.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.105

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
B

Cadherin-3