SMTL ID : 5k6v.1

Sidekick-1 immunoglobulin domains 1-4, crystal form 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.48, L.69, A.71, F.73 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain B: N.48, L.69, A.71, F.73 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.178 Chain B: Y.59 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: Y.59 Chain B: N.178 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.208, F.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.208 NAG.12: 2 residues within 4Å: Chain B: N.208, F.286 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.208

12 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.23 Chain B: H.23, N.27 Ligands: ZN.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.23, B:H.23 ZN.5: 1 residues within 4Å: Chain A: D.381 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.381, H2O.1 ZN.6: 3 residues within 4Å: Chain A: D.191, T.192, H.195 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.191 ZN.7: 2 residues within 4Å: Chain A: H.113, A.114 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Chain A: D.104, H.185 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.104, A:H.185 ZN.9: 1 residues within 4Å: Chain A: H.248 No protein-ligand interaction detected (PLIP) ZN.13: 4 residues within 4Å: Chain A: H.23, N.27 Chain B: H.23 Ligands: ZN.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.23, B:H.23 ZN.14: 1 residues within 4Å: Chain B: D.381 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.381, H2O.1 ZN.15: 3 residues within 4Å: Chain B: D.191, T.192, H.195 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.191 ZN.16: 2 residues within 4Å: Chain B: H.113, A.114 No protein-ligand interaction detected (PLIP) ZN.17: 2 residues within 4Å: Chain B: D.104, H.185 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.104, B:H.185 ZN.18: 1 residues within 4Å: Chain B: H.248 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodman, K.M. et al., Molecular basis of sidekick-mediated cell-cell adhesion and specificity. Elife (2016)

Release Date

2016-09-28

Peptides

Protein sidekick-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein sidekick-1

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