SMTL ID : 4xb8.1

Crystal structure of Dscam1 isoform 9.44, N-terminal four Ig domains (with zinc)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 8 residues within 4Å: Chain A: N.22, S.23, P.69, F.70, R.71, A.72, V.106, I.107 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: 4 residues within 4Å: Chain A: Y.250, N.297, G.302, E.303 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: Y.250, V.295, N.297, G.302, E.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.263

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: N.16, D.99, H.101, R.380 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.99, A:D.99, A:H.101, H2O.1 ZN.5: 2 residues within 4Å: Chain A: E.13, E.387 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.13, A:E.13, A:E.387, A:E.387 ZN.6: 4 residues within 4Å: Chain A: E.113, E.130 Chain B: D.115, N.116 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.113, A:E.130, A:E.130, B:D.115, B:D.115 ZN.7: 5 residues within 4Å: Chain A: D.115, N.116 Chain B: E.113, D.115, E.130 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.113, B:E.130, B:E.130, A:D.115, A:D.115 ZN.9: 2 residues within 4Å: Chain B: D.99, H.101 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.99, B:D.99, B:H.101, H2O.1 ZN.10: 2 residues within 4Å: Chain B: E.13, E.387 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.13, B:E.13, B:E.387, B:E.387

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

NAG.8: 5 residues within 4Å: Chain B: N.22, S.23, R.71, A.72, V.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.22

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 9.44: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Down Syndrome Cell Adhesion Molecule, isoform 9.44

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