SMTL ID : 3q2w.1

Crystal structure of mouse N-cadherin ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: K.408, N.409, I.411, N.413, Q.433 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain B: N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain B: K.408, N.409, I.411, N.413, Q.433 No protein-ligand interaction detected (PLIP)

24 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.11, D.67, E.69, D.103 Ligands: CA.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.11, A:D.67, A:E.69, A:D.103 CA.4: 8 residues within 4Å: Chain A: E.11, E.69, D.100, M.101, D.103, N.104, D.136 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:E.69, A:D.100, A:D.103, A:D.136 CA.5: 6 residues within 4Å: Chain A: N.102, N.104, D.134, D.136, N.142, D.194 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.104, A:D.134, A:D.136, A:N.142, A:D.194 CA.6: 6 residues within 4Å: Chain A: E.119, E.181, D.215, V.216, D.218, D.250 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.119, A:E.181, A:V.216, A:D.218, A:D.250 CA.7: 6 residues within 4Å: Chain A: N.217, N.219, D.248, D.250, A.256, N.307 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.219, A:D.248, A:D.248, A:D.250, A:A.256 CA.8: 4 residues within 4Å: Chain A: E.119, D.179, E.181, D.218 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.119, A:D.179, A:E.181, A:D.218 CA.9: 4 residues within 4Å: Chain A: E.234, D.292, E.294, E.334 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.234, A:D.292, A:E.294, A:E.334 CA.10: 6 residues within 4Å: Chain A: E.234, E.294, D.331, V.332, E.334, D.366 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.234, A:E.294, A:D.331, A:V.332, A:E.334 CA.11: 6 residues within 4Å: Chain A: N.333, E.334, D.364, D.366, Q.371, D.420 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.334, A:D.364, A:D.420 CA.12: 7 residues within 4Å: Chain A: E.349, E.403, D.438, I.439, D.441, N.442, D.470 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.349, A:E.403, A:D.438, A:D.441, A:D.470 CA.13: 4 residues within 4Å: Chain A: E.349, D.401, E.403, D.441 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.349, A:D.401, A:E.403, A:D.441 CA.14: 6 residues within 4Å: Chain A: N.440, N.442, D.468, D.470, N.474, D.525 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.442, A:D.468, A:D.468, A:D.470, A:D.525 CA.29: 5 residues within 4Å: Chain B: E.11, D.67, E.69, D.103 Ligands: CA.30 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.11, B:D.67, B:E.69, B:D.103 CA.30: 8 residues within 4Å: Chain B: E.11, E.69, D.100, M.101, D.103, N.104, D.136 Ligands: CA.29 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:E.69, B:D.100, B:D.103, B:D.136 CA.31: 6 residues within 4Å: Chain B: N.102, N.104, D.134, D.136, N.142, D.194 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.104, B:D.134, B:D.136, B:N.142, B:D.194 CA.32: 6 residues within 4Å: Chain B: E.119, E.181, D.215, V.216, D.218, D.250 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.119, B:E.181, B:V.216, B:D.218, B:D.250 CA.33: 6 residues within 4Å: Chain B: N.217, N.219, D.248, D.250, A.256, N.307 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.219, B:D.248, B:D.248, B:D.250, B:A.256 CA.34: 4 residues within 4Å: Chain B: E.119, D.179, E.181, D.218 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.119, B:D.179, B:E.181, B:D.218 CA.35: 4 residues within 4Å: Chain B: E.234, D.292, E.294, E.334 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.234, B:D.292, B:E.294, B:E.334 CA.36: 6 residues within 4Å: Chain B: E.234, E.294, D.331, V.332, E.334, D.366 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.234, B:E.294, B:D.331, B:V.332, B:E.334 CA.37: 6 residues within 4Å: Chain B: N.333, E.334, D.364, D.366, Q.371, D.420 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.334, B:D.364, B:D.420 CA.38: 7 residues within 4Å: Chain B: E.349, E.403, D.438, I.439, D.441, N.442, D.470 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.349, B:E.403, B:D.438, B:D.441, B:D.470 CA.39: 4 residues within 4Å: Chain B: E.349, D.401, E.403, D.441 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.349, B:D.401, B:E.403, B:D.441 CA.40: 6 residues within 4Å: Chain B: N.440, N.442, D.468, D.470, N.474, D.525 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.442, B:D.468, B:D.468, B:D.470, B:D.525

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

MAN.15: 4 residues within 4Å: Chain A: Q.111, I.189, T.206 Ligands: MAN.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.111 MAN.16: 5 residues within 4Å: Chain A: Q.111, V.112, I.189, T.208 Ligands: MAN.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.111 MAN.17: 4 residues within 4Å: Chain A: L.109, W.113, T.129, T.131 No protein-ligand interaction detected (PLIP) MAN.18: 3 residues within 4Å: Chain A: Y.229, V.300, S.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.229, A:Y.229 MAN.19: 4 residues within 4Å: Chain A: M.226, T.227, T.302, T.324 No protein-ligand interaction detected (PLIP) MAN.20: 3 residues within 4Å: Chain A: H.317, P.318, T.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.317, A:H.317 MAN.21: 3 residues within 4Å: Chain A: L.417, S.427 Ligands: MAN.22 No protein-ligand interaction detected (PLIP) MAN.22: 4 residues within 4Å: Chain A: L.417, T.429 Ligands: MAN.21, MAN.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.429 MAN.23: 4 residues within 4Å: Chain A: T.415, T.429, T.431 Ligands: MAN.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.429 MAN.41: 4 residues within 4Å: Chain B: Q.111, I.189, T.206 Ligands: MAN.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.111 MAN.42: 5 residues within 4Å: Chain B: Q.111, V.112, I.189, T.208 Ligands: MAN.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.111 MAN.43: 4 residues within 4Å: Chain B: L.109, W.113, T.129, T.131 No protein-ligand interaction detected (PLIP) MAN.44: 3 residues within 4Å: Chain B: Y.229, V.300, S.326 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.229 MAN.45: 4 residues within 4Å: Chain B: M.226, T.227, T.302, T.324 No protein-ligand interaction detected (PLIP) MAN.46: 3 residues within 4Å: Chain B: H.317, P.318, T.322 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.317, B:H.317 MAN.47: 3 residues within 4Å: Chain B: L.417, S.427 Ligands: MAN.48 No protein-ligand interaction detected (PLIP) MAN.48: 4 residues within 4Å: Chain B: L.417, T.429 Ligands: MAN.47, MAN.49 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.429 MAN.49: 4 residues within 4Å: Chain B: T.415, T.429, T.431 Ligands: MAN.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.429

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

NAG.24: 3 residues within 4Å: Chain A: H.110, V.112, N.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.114, A:N.114 NAG.25: 3 residues within 4Å: Chain A: N.243, D.282, L.284 No protein-ligand interaction detected (PLIP) NAG.26: 3 residues within 4Å: Chain A: N.492, W.493, E.518 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.488, A:T.488 NAG.50: 3 residues within 4Å: Chain B: H.110, V.112, N.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.114, B:N.114 NAG.51: 3 residues within 4Å: Chain B: N.243, D.282, L.284 No protein-ligand interaction detected (PLIP) NAG.52: 3 residues within 4Å: Chain B: N.492, W.493, E.518 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure (2011)

Release Date

2011-02-23

Peptides

Cadherin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cadherin-2