SMTL ID : 3ubf.3 (2 other biounits)

Crystal structure of Drosophila N-cadherin EC1-3, I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

36 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: E.13, E.61, D.98, D.136, H.139 Ligands: ZN.16, CA.19 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.61, A:D.98, A:D.98, A:D.136, H2O.6 ZN.2: 2 residues within 4Å: Chain A: H.142, E.158 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.142, A:E.158 ZN.3: 1 residues within 4Å: Chain A: D.157 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.157 ZN.4: 2 residues within 4Å: Chain A: D.243 Chain B: E.222 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.243, H2O.1, H2O.5 ZN.5: 1 residues within 4Å: Chain A: D.304 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.304, A:D.304 ZN.6: 4 residues within 4Å: Chain A: D.134, H.139, D.185, Q.196 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.134, A:D.134, A:H.139, A:D.185 ZN.7: 3 residues within 4Å: Chain A: D.59, E.62, D.138 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:D.59, A:D.138, H2O.4, H2O.4 ZN.8: 1 residues within 4Å: Chain A: E.102 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.102, H2O.5 ZN.9: 2 residues within 4Å: Chain A: E.200 Ligands: ZN.28 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.200, H2O.4, H2O.11 ZN.10: 1 residues within 4Å: Chain A: D.169 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.169, H2O.6 ZN.11: 2 residues within 4Å: Chain A: V.312 Ligands: ZN.18 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.312, H2O.6 ZN.12: 2 residues within 4Å: Chain A: E.245, T.265 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.245 ZN.13: 1 residues within 4Å: Chain A: S.1 No protein-ligand interaction detected (PLIP) ZN.14: 4 residues within 4Å: Chain A: E.225, E.278, D.311 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.225, A:E.225, A:E.278, A:D.311, H2O.1 ZN.15: 2 residues within 4Å: Chain A: D.279, R.281 No protein-ligand interaction detected (PLIP) ZN.16: 6 residues within 4Å: Chain A: E.13, N.100, D.136, D.138 Ligands: ZN.1, CA.19 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.136, H2O.6 ZN.17: 3 residues within 4Å: Chain A: D.232 Chain B: D.232 Ligands: ZN.36 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.232, A:D.232, A:D.232 ZN.18: 4 residues within 4Å: Chain A: E.278, D.311 Ligands: ZN.11, ZN.14 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.311, H2O.6 ZN.20: 7 residues within 4Å: Chain B: E.13, E.61, D.98, D.136, H.139 Ligands: ZN.35, CA.38 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.61, B:D.98, B:D.98, B:D.136, H2O.13 ZN.21: 2 residues within 4Å: Chain B: H.142, E.158 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.142, B:E.158 ZN.22: 1 residues within 4Å: Chain B: D.157 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.157 ZN.23: 2 residues within 4Å: Chain A: E.222 Chain B: D.243 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.243, H2O.7, H2O.12 ZN.24: 1 residues within 4Å: Chain B: D.304 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.304, B:D.304 ZN.25: 4 residues within 4Å: Chain B: D.134, H.139, D.185, Q.196 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.134, B:D.134, B:H.139, B:D.185 ZN.26: 3 residues within 4Å: Chain B: D.59, E.62, D.138 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:D.59, B:D.138, H2O.10, H2O.10 ZN.27: 1 residues within 4Å: Chain B: E.102 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.102, H2O.11 ZN.28: 2 residues within 4Å: Chain B: E.200 Ligands: ZN.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.200, H2O.4, H2O.11 ZN.29: 1 residues within 4Å: Chain B: D.169 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.169, H2O.13 ZN.30: 2 residues within 4Å: Chain B: V.312 Ligands: ZN.37 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.312, H2O.12 ZN.31: 2 residues within 4Å: Chain B: E.245, T.265 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.245 ZN.32: 1 residues within 4Å: Chain B: S.1 No protein-ligand interaction detected (PLIP) ZN.33: 4 residues within 4Å: Chain B: E.225, E.278, D.311 Ligands: ZN.37 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.225, B:E.225, B:E.278, B:D.311, H2O.8 ZN.34: 2 residues within 4Å: Chain B: D.279, R.281 No protein-ligand interaction detected (PLIP) ZN.35: 6 residues within 4Å: Chain B: E.13, N.100, D.136, D.138 Ligands: ZN.20, CA.38 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.136, H2O.13 ZN.36: 3 residues within 4Å: Chain A: D.232 Chain B: D.232 Ligands: ZN.17 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.232, B:D.232, A:D.232 ZN.37: 4 residues within 4Å: Chain B: E.278, D.311 Ligands: ZN.30, ZN.33 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.311, H2O.12

2 x CA: CALCIUM ION(Non-covalent)

CA.19: 6 residues within 4Å: Chain A: E.13, D.59, E.61, D.138 Ligands: ZN.1, ZN.16 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.13, A:D.59, A:E.61, H2O.4, H2O.6 CA.38: 6 residues within 4Å: Chain B: E.13, D.59, E.61, D.138 Ligands: ZN.20, ZN.35 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.13, B:D.59, B:E.61, H2O.11, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, X. et al., Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca2+-free interdomain linkers. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2011-12-21

Peptides

Neural-cadherin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Neural-cadherin

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