SMTL ID : 4x9f.1

Crystal structure of Dscam1 isoform 6.9, N-terminal four Ig domains

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 7 residues within 4Å: Chain A: N.22, S.23, P.69, F.70, R.71, A.72, V.106 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 11 residues within 4Å: Chain A: K.342, T.343, S.345, R.378 Chain B: R.250, V.293, V.294, N.295, G.300, E.301, S.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.342, A:K.342, A:K.342 Water bridges: A:V.344

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.2: 7 residues within 4Å: Chain A: L.291, V.293, V.294, N.295, G.300, E.301 Chain B: D.380 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.380 Hydrophobic interactions: A:L.291 NAG-NAG-BMA.3: 8 residues within 4Å: Chain B: N.22, S.23, F.70, R.71, A.72, V.106, N.107, F.109 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.109

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 12 residues within 4Å: Chain A: A.124, V.126, H.171, L.238, C.239, M.240, A.241, V.273, S.274, G.275, T.276 Ligands: GOL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.171, A:C.239, A:C.239, A:A.241, A:G.275, A:T.276 GOL.6: 8 residues within 4Å: Chain A: E.117, A.124, A.125, V.126, M.240, A.241, Q.242 Ligands: GOL.5 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.126, A:V.126, A:A.241, A:Q.242 Water bridges: B:S.133 GOL.15: 4 residues within 4Å: Chain A: Y.75, R.76, Q.77, E.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76, A:R.76 GOL.16: 11 residues within 4Å: Chain B: A.124, V.126, H.171, L.238, C.239, M.240, A.241, V.273, S.274, G.275, T.276 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:C.239, B:A.241, B:A.241, B:G.275, B:T.276, B:T.276, B:T.276

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

SO4.7: 4 residues within 4Å: Chain A: S.213 Chain B: Y.75 Ligands: SO4.17, SO4.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.75, A:S.213 SO4.8: 6 residues within 4Å: Chain A: R.173, S.274 Ligands: SO4.9, SO4.10, SO4.11, SO4.12 No protein-ligand interaction detected (PLIP) SO4.9: 2 residues within 4Å: Chain A: R.173 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.173, A:R.173 SO4.10: 2 residues within 4Å: Chain A: Q.272 Ligands: SO4.8 No protein-ligand interaction detected (PLIP) SO4.11: 1 residues within 4Å: Ligands: SO4.8 No protein-ligand interaction detected (PLIP) SO4.12: 4 residues within 4Å: Chain A: R.173, V.273, S.274 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.173 SO4.17: 4 residues within 4Å: Ligands: SO4.7, SO4.18, SO4.19, SO4.20 No protein-ligand interaction detected (PLIP) SO4.18: 3 residues within 4Å: Chain B: Q.77 Ligands: SO4.17, SO4.19 No protein-ligand interaction detected (PLIP) SO4.19: 6 residues within 4Å: Chain B: Y.75, R.76, Q.77 Ligands: SO4.7, SO4.17, SO4.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.75, B:Q.77 Water bridges: B:E.78 SO4.20: 2 residues within 4Å: Chain B: R.76 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.76 SO4.21: 5 residues within 4Å: Chain B: R.76 Ligands: SO4.22, SO4.23, SO4.24, SO4.25 No protein-ligand interaction detected (PLIP) SO4.22: 2 residues within 4Å: Chain B: R.76 Ligands: SO4.21 No protein-ligand interaction detected (PLIP) SO4.23: 3 residues within 4Å: Chain B: V.53, R.76 Ligands: SO4.21 No protein-ligand interaction detected (PLIP) SO4.24: 1 residues within 4Å: Ligands: SO4.21 No protein-ligand interaction detected (PLIP) SO4.25: 4 residues within 4Å: Chain B: L.56, D.74, R.76 Ligands: SO4.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.74, B:R.76

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.13: 3 residues within 4Å: Chain A: V.53, P.54, L.56 No protein-ligand interaction detected (PLIP) EPE.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S.A. et al., Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition. Sci Adv (2016)

Release Date

2015-12-16

Peptides

Down Syndrome Cell Adhesion Molecule isoform 6.9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Down Syndrome Cell Adhesion Molecule isoform 6.9