SMTL ID : 7stz.1

Crystal Structure of Human E-cadherin EC1-5 bound by mouse monoclonal antibody Fab mAb-1_19A11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-2-2-2-mer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: A.88, T.113, V.114, T.115, N.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.88, A:T.115 Water bridges: A:D.116, A:N.156 EDO.26: 5 residues within 4Å: Chain B: Q.22, K.24, T.42, V.43, S.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.22 EDO.27: 5 residues within 4Å: Chain B: S.84, R.85, L.86, S.87, N.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.102 Water bridges: B:L.86 EDO.47: 4 residues within 4Å: Chain E: Y.78, K.83, S.84, L.86 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.84 EDO.48: 5 residues within 4Å: Chain E: M.111, G.131, T.132, S.133, P.174 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.132, E:S.133 Water bridges: E:G.131

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

NAG.2: 4 residues within 4Å: Chain A: A.496, N.499, L.520, Y.525 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.496, A:Y.525, A:Y.525

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

PG4.3: 4 residues within 4Å: Chain A: D.154, V.155, N.156, Y.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.154, A:V.155 PG4.4: 4 residues within 4Å: Chain A: S.497, T.501, K.515, K.517 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.515, A:K.517 Water bridges: A:S.497, A:K.517 PG4.28: 9 residues within 4Å: Chain B: L.64, E.65, W.66, N.79 Chain C: H.122, T.123, F.124, G.125, G.126 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:W.66, C:H.122, C:F.124 PG4.29: 5 residues within 4Å: Chain D: D.154, V.155, N.156, T.157, A.161 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.184 PG4.49: 8 residues within 4Å: Chain E: G.63, L.64, E.65, W.66, N.79 Chain F: T.123, F.124, G.126 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.63, E:G.63, E:W.66, E:N.79 Water bridges: E:W.66

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

MAN.5: 2 residues within 4Å: Chain A: T.220 Ligands: BMA.6 No protein-ligand interaction detected (PLIP) MAN.7: 5 residues within 4Å: Chain A: L.278, A.317, T.330, T.332 Ligands: BMA.8 No protein-ligand interaction detected (PLIP) MAN.11: 5 residues within 4Å: Chain A: W.388, T.438, T.440 Ligands: BMA.9, BMA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.438

12 x BMA: beta-D-mannopyranose(Post Translational Modification)

BMA.6: 5 residues within 4Å: Chain A: E.127, V.128, V.206, T.222 Ligands: MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.127 BMA.8: 4 residues within 4Å: Chain A: T.319, L.328, T.330 Ligands: MAN.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.328, A:T.330 BMA.9: 6 residues within 4Å: Chain A: P.351, E.352, L.426, G.441, T.442 Ligands: MAN.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.351 BMA.10: 3 residues within 4Å: Chain A: W.388, T.438 Ligands: MAN.11 No protein-ligand interaction detected (PLIP) BMA.12: 5 residues within 4Å: Chain A: S.142, V.143, M.144, E.145, V.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.142, A:E.145 BMA.13: 5 residues within 4Å: Chain A: T.240, T.241, T.332, A.333, T.334 No protein-ligand interaction detected (PLIP) BMA.30: 2 residues within 4Å: Chain D: T.220 Ligands: BMA.31 No protein-ligand interaction detected (PLIP) BMA.31: 6 residues within 4Å: Chain D: E.127, V.128, T.220, A.221, T.222 Ligands: BMA.30 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.127, D:T.220, D:A.221 BMA.32: 4 residues within 4Å: Chain D: L.278, T.330, T.332 Ligands: BMA.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.330 BMA.33: 3 residues within 4Å: Chain D: T.329, T.330 Ligands: BMA.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.330 BMA.34: 5 residues within 4Å: Chain D: S.142, V.143, M.144, E.145, V.187 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.143, D:E.145 BMA.35: 4 residues within 4Å: Chain D: H.315, T.332, A.333, T.334 No protein-ligand interaction detected (PLIP)

24 x CA: CALCIUM ION(Non-covalent)

CA.14: 7 residues within 4Å: Chain A: E.27, E.85, D.116, Q.117, D.119, N.120, D.152 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.27, A:E.85, A:E.85, A:D.116, A:Q.117 CA.15: 4 residues within 4Å: Chain A: E.27, D.83, E.85, D.119 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.27, A:D.83, A:E.85, A:D.119 CA.16: 6 residues within 4Å: Chain A: N.118, N.120, D.150, D.152, N.159, D.211 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.120, A:D.150, A:D.152, A:N.159, A:D.211 CA.17: 6 residues within 4Å: Chain A: N.231, N.233, D.262, D.264, A.270, N.320 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.233, A:D.262, A:D.262, A:D.264, A:A.270 CA.18: 6 residues within 4Å: Chain A: E.248, E.307, D.341, V.342, E.344, D.376 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.248, A:E.307, A:D.341, A:V.342, A:E.344, A:D.376 CA.19: 7 residues within 4Å: Chain A: N.343, E.344, E.374, D.376, Q.381, D.431, N.432 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.374, A:E.374, A:D.431 CA.20: 6 residues within 4Å: Chain A: N.451, N.453, D.478, D.480, N.484, D.533 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.453, A:D.478, A:D.480, A:N.484, A:D.533 CA.21: 6 residues within 4Å: Chain A: E.359, E.413, D.449, V.450, D.452, D.480 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.359, A:E.413, A:D.449, A:V.450, A:D.452, A:D.480 CA.22: 4 residues within 4Å: Chain A: E.359, D.411, E.413, D.452 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.359, A:D.411, A:E.413, A:D.452, A:D.452 CA.23: 8 residues within 4Å: Chain A: E.135, R.197, E.198, D.229, T.230, D.232, D.264 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.135, A:D.229, A:T.230, A:D.232, A:D.264 CA.24: 5 residues within 4Å: Chain A: E.135, D.196, E.198, D.232 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.135, A:D.196, A:D.196, A:E.198, A:D.232 CA.25: 4 residues within 4Å: Chain A: E.248, D.305, E.307, E.344 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.248, A:D.305, A:D.305, A:E.307, A:E.344 CA.36: 5 residues within 4Å: Chain D: E.248, E.307, V.342, E.344, D.376 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.248, D:E.307, D:E.307, D:V.342, D:E.344 CA.37: 7 residues within 4Å: Chain D: E.135, E.198, D.229, T.230, D.232, D.264 Ligands: CA.44 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.135, D:E.198, D:D.229, D:T.230, D:D.232 CA.38: 6 residues within 4Å: Chain D: N.343, E.344, E.374, D.376, Q.381, D.431 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.374, D:D.376, D:D.431 CA.39: 5 residues within 4Å: Chain D: E.27, D.83, E.85, D.119, N.120 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.27, D:D.83, D:E.85, D:D.119 CA.40: 7 residues within 4Å: Chain D: E.27, E.85, D.116, Q.117, D.119, N.120, D.152 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.85, D:D.116, D:Q.117, D:D.119, D:D.152 CA.41: 6 residues within 4Å: Chain D: N.118, N.120, D.150, D.152, N.159, D.211 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:N.120, D:D.150, D:D.152, D:N.159, D:D.211 CA.42: 6 residues within 4Å: Chain D: N.231, N.233, D.262, D.264, A.270, N.320 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:N.233, D:D.262, D:D.262, D:D.264, D:A.270 CA.43: 4 residues within 4Å: Chain D: E.359, R.412, E.413 Ligands: CA.46 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.359, D:E.413 CA.44: 5 residues within 4Å: Chain D: E.135, D.196, E.198, D.232 Ligands: CA.37 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.135, D:E.135, D:E.198, D:D.232, D:D.232 CA.45: 4 residues within 4Å: Chain D: E.248, D.305, E.307, E.344 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.305, D:E.344 CA.46: 6 residues within 4Å: Chain D: E.359, E.413, V.450, N.451, D.452 Ligands: CA.43 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.359, D:E.359, D:E.413, D:V.450, D:D.452 CA.50: 3 residues within 4Å: Chain E: S.203 Chain F: S.202, T.204 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maker, A. et al., Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography. Pnas Nexus (2022)

Release Date

2022-01-26

Peptides

Cadherin-1: AD
mAb-1_19A11 Heavy Chain: BE
mAb-1_19A11 Light Chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
D

B
H

E
I

C
L

F
M

Cadherin-1

mAb-1_19A11 Heavy Chain

mAb-1_19A11 Light Chain