SMTL ID : 4zmv.1

Crystal structure of human P-cadherin (ss-X-dimer pocket I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.2: 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:D.101, A:Q.102, A:D.104, A:D.137 CA.8: 7 residues within 4Å: Chain B: E.12, E.70, D.101, Q.102, D.104, H.105, D.137 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.12, B:E.70, B:Q.102, B:D.104, B:D.137 CA.9: 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

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

NI.3: 4 residues within 4Å: Chain A: H.105, E.136 Ligands: SO4.5, SO4.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.105 NI.4: 2 residues within 4Å: Chain A: M.1 Chain B: M.1 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:M.1, A:M.1, H2O.2 NI.10: 4 residues within 4Å: Chain B: H.105, E.136 Ligands: SO4.11, SO4.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.105, H2O.2

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

SO4.5: 6 residues within 4Å: Chain A: D.68, E.70, H.105, E.136 Ligands: NI.3, SO4.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.105 SO4.6: 5 residues within 4Å: Chain A: D.68, D.104, H.105 Ligands: NI.3, SO4.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.105 SO4.11: 5 residues within 4Å: Chain B: D.68, D.104, H.105 Ligands: NI.10, SO4.12 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.105 SO4.12: 6 residues within 4Å: Chain B: D.68, E.70, H.105, E.136 Ligands: NI.10, SO4.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.105

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: Y.143, M.197, D.198, D.200 Chain B: N.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.13, B:N.13, A:M.197 GOL.13: 4 residues within 4Å: Chain A: N.13 Chain B: Y.143, M.197, D.200 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.197, A:N.13, A:N.13

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