SMTL ID : 4zte.1

Crystal structure of human E-Cadherin (residues 3-213) in complex with a peptidomimetic inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: N.100, N.102, D.132, D.134, N.141, D.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.102, A:D.132, A:D.134, A:N.141, A:D.193 CA.2: 8 residues within 4Å: Chain A: E.9, E.67, D.98, Q.99, D.101, N.102, D.134 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:D.98, A:Q.99, A:D.101, A:D.134 CA.3: 5 residues within 4Å: Chain A: E.9, D.65, E.67, D.101 Ligands: CA.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.9, A:D.65, A:E.67, A:D.101, H2O.4, H2O.5 CA.5: 6 residues within 4Å: Chain B: N.100, N.102, D.132, D.134, N.141, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.102, B:D.132, B:D.134, B:N.141, B:D.193 CA.6: 8 residues within 4Å: Chain B: E.9, E.67, D.98, Q.99, D.101, N.102, D.134 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.67, B:E.67, B:D.98, B:D.134 CA.7: 5 residues within 4Å: Chain B: E.9, D.65, E.67, D.101 Ligands: CA.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.9, B:D.65, B:E.67, B:D.101, H2O.6, H2O.9

2 x 4RL: N-{[(2S,5S)-1-benzyl-5-(2-{[(2S,3S)-1-(tert-butylamino)-3-methyl-1-oxopentan-2-yl]amino}-2-oxoethyl)-3,6-dioxopiperazin-2-yl]methyl}-L-alpha-asparagine(Non-covalent)

4RL.4: 15 residues within 4Å: Chain A: I.2, P.4, I.5, S.6, C.7, P.8, L.19, T.97 Chain B: P.3, P.4, I.5, S.6, P.8, E.11 Ligands: 4RL.8 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.2, A:L.19, A:T.97, B:P.3 Hydrogen bonds: A:S.6 4RL.8: 15 residues within 4Å: Chain A: P.3, P.4, S.6, C.7, P.8 Chain B: I.2, P.3, P.4, I.5, S.6, N.18, L.19, T.95, T.97 Ligands: 4RL.4 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.2, B:I.5, B:T.97, A:P.3, A:P.8 Hydrogen bonds: B:S.6, B:S.6, B:S.6, A:P.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nardone, V. et al., Crystal Structure of Human E-Cadherin-EC1EC2 in Complex with a Peptidomimetic Competitive Inhibitor of Cadherin Homophilic Interaction. J.Med.Chem. (2016)

Release Date

2016-06-01

Peptides

Cadherin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cadherin-1

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