SMTL ID : 6efz.1

Crystal Structure of DIP-Theta Ig1-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[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-MAN-FUC.1: 5 residues within 4Å: Chain A: N.11, T.13, W.82, Y.98, D.100 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.98 NAG-NAG-BMA-MAN-MAN-FUC.7: 5 residues within 4Å: Chain B: N.11, T.13, W.82, Y.98, D.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.100 Hydrophobic interactions: B:Y.98

2 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: 4 residues within 4Å: Chain A: N.123, P.151, T.165, A.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.8: 4 residues within 4Å: Chain B: N.123, P.151, T.165, A.167 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: A.158, N.160 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain B: A.158, N.160 No protein-ligand interaction detected (PLIP)

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

ACT.4: 4 residues within 4Å: Chain A: N.55, R.57, K.76 Chain B: D.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.55 Salt bridges: A:R.57, A:K.76 ACT.5: 2 residues within 4Å: Chain A: K.76, S.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.78 ACT.10: 4 residues within 4Å: Chain A: D.90 Chain B: N.55, R.57, K.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.55 Salt bridges: B:R.57, B:K.76 ACT.11: 2 residues within 4Å: Chain B: K.76, S.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.78

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

PEG.6: 5 residues within 4Å: Chain A: D.27, N.28, L.29, K.65, R.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.27, A:N.28 PEG.12: 5 residues within 4Å: Chain B: D.27, N.28, L.29, K.65, R.66 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.27, B:D.27, B:N.28

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

Dpr-interacting protein theta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dpr-interacting protein theta

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