SMTL ID : 5k6x.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

NAG-FUC.1: 3 residues within 4Å: Chain A: N.208, Y.286, S.288 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.286 Hydrogen bonds: A:S.288, A:S.288

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 5 residues within 4Å: Chain B: N.208, G.284, A.285, Y.286, S.288 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.286 Hydrogen bonds: B:S.288, B:S.288

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

NAG.3: 4 residues within 4Å: Chain A: Q.169, N.178 Chain B: L.57, Y.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.169 NAG.13: 4 residues within 4Å: Chain A: Y.59 Chain B: Q.169, N.178, T.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.169, B:T.180

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

SO4.4: 8 residues within 4Å: Chain A: K.14, C.33, M.34, A.35, E.36, Y.59 Chain B: Q.169, V.171 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.35, A:A.35, B:Q.169 Water bridges: A:K.14, B:T.131 Salt bridges: A:K.14 SO4.5: 1 residues within 4Å: Chain A: R.60 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.60 SO4.6: 4 residues within 4Å: Chain A: H.111, V.159, A.160, P.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.160 Salt bridges: A:H.111 SO4.7: 3 residues within 4Å: Chain A: S.142, R.144, I.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.142 Salt bridges: A:R.144 SO4.8: 3 residues within 4Å: Chain A: S.142, S.143, Y.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.143, A:S.143, A:Y.250 SO4.9: 3 residues within 4Å: Chain A: M.62, I.63, T.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.64, A:T.64 SO4.10: 4 residues within 4Å: Chain A: V.18, R.19, T.20 Chain B: S.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.19, A:T.20 SO4.11: 2 residues within 4Å: Chain A: R.345, S.346 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.346, A:S.346 SO4.14: 5 residues within 4Å: Chain B: R.75, Y.328, F.366, H.368, E.373 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.328 Salt bridges: B:R.75 SO4.15: 8 residues within 4Å: Chain A: V.171 Chain B: K.14, C.33, M.34, A.35, E.36, F.43, Y.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.35, B:A.35, B:E.36 Salt bridges: B:K.14 SO4.16: 2 residues within 4Å: Chain B: R.50, E.51 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.51 SO4.17: 3 residues within 4Å: Chain B: V.18, R.19, T.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.19, B:T.20

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: H.23, L.24, N.27 Chain B: H.23, L.24, N.27 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.22, A:H.23, A:L.24, A:N.27, B:L.24, B:N.27

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-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein sidekick-2

Related Entries With Identical Sequence