SMTL ID : 6eg0.1

Crystal structure of Dpr4 Ig1-Ig2 in complex with DIP-Eta Ig1-Ig3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 4 residues within 4Å: Chain A: L.122, N.136, T.138, L.182 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.2: 6 residues within 4Å: Chain A: G.156, K.157, N.193, T.195, S.203, S.205 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-FUC.3: 5 residues within 4Å: Chain B: N.21, T.23, W.92, Y.108, D.110 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.23, B:Y.108

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

NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.4: 4 residues within 4Å: Chain B: N.261, T.263, S.271, R.273 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.273

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

NAG.5: 1 residues within 4Å: Chain B: N.133 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 3 residues within 4Å: Chain B: V.49, W.92, M.106 No protein-ligand interaction detected (PLIP) PEG.7: 3 residues within 4Å: Chain B: E.233, I.265, R.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.269

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain B: R.288, V.290, D.297, T.298, D.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.288, B:R.288, B:D.299

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 7 residues within 4Å: Chain A: E.103 Chain B: R.48, L.55, N.65, R.67, D.89, Y.93 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.55 Hydrogen bonds: B:N.65, B:R.67, B:Y.93 Salt bridges: B:R.48 ACT.10: 3 residues within 4Å: Chain B: G.185, T.204, V.206 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cosmanescu, F. et al., Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins. Neuron (2018)

Release Date

2018-11-28

Peptides

Defective proboscis extension response 4: A
Dpr-interacting protein eta, isoform B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Defective proboscis extension response 4

Dpr-interacting protein eta, isoform B