SMTL ID : 5k6w.1

Sidekick-1 immunoglobulin domains 1-5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: N.208, R.209, F.286, S.288 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.286 Hydrogen bonds: A:S.288 NAG-FUC.4: 5 residues within 4Å: Chain B: N.208, S.210, F.286, L.287, S.288 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.286 Hydrogen bonds: B:S.210, B:S.288

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: 4 residues within 4Å: Chain A: N.48, L.69, A.71, E.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.91 NAG-NAG.3: 4 residues within 4Å: Chain B: R.47, N.48, A.71, F.73 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: Q.169, N.178 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.457 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.470 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain B: N.470 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.470 NAG.11: 3 residues within 4Å: Chain B: N.178, K.179, T.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.178, B:T.180

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: Q.21, H.23, L.24, N.27 Chain B: H.23, L.24, N.27, R.28 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.21, A:H.23, A:L.24, A:N.27, B:L.24, B:N.27, B:R.28 GOL.12: 4 residues within 4Å: Chain A: S.301 Chain B: H.248, S.249, Y.250 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.248, B:S.249, A:S.301

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 4 residues within 4Å: Chain A: R.75, Q.326, Y.328, E.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.328 Salt bridges: A:R.75 SO4.13: 3 residues within 4Å: Chain B: S.142, R.144, I.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.142 Salt bridges: B:R.144 SO4.14: 4 residues within 4Å: Chain B: A.10, P.11, S.301, H.377 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.10, B:S.301 Salt bridges: B:H.377

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
B

Protein sidekick-1