SMTL ID : 4oum.1

Crystal structure of human Caprin-2 C1q domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-trimer

Ligands

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 4 residues within 4Å: Chain A: W.119 Ligands: FLC.2, IPA.3, IPA.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.117 PG4.6: 4 residues within 4Å: Chain B: W.119 Ligands: FLC.7, IPA.8, IPA.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.117 PG4.11: 4 residues within 4Å: Chain C: W.119 Ligands: FLC.12, IPA.13, IPA.14 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.117

3 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 7 residues within 4Å: Chain A: W.119, Y.121 Chain B: Y.66, H.110, R.111 Ligands: PG4.1, IPA.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.119 Hydrogen bonds: A:Y.121, A:Y.121 Water bridges: A:S.117 Salt bridges: B:H.110, B:R.111 FLC.7: 7 residues within 4Å: Chain B: W.119, Y.121 Chain C: Y.66, H.110, R.111 Ligands: PG4.6, IPA.8 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Salt bridges: C:H.110, C:R.111 Hydrophobic interactions: B:W.119 Hydrogen bonds: B:Y.121, B:Y.121 Water bridges: B:S.117 FLC.12: 7 residues within 4Å: Chain A: Y.66, H.110, R.111 Chain C: W.119, Y.121 Ligands: PG4.11, IPA.13 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.119 Hydrogen bonds: C:Y.121, C:Y.121 Water bridges: C:S.117 Salt bridges: A:H.110, A:R.111

9 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 3 residues within 4Å: Ligands: PG4.1, FLC.2, IPA.4 No protein-ligand interaction detected (PLIP) IPA.4: 2 residues within 4Å: Ligands: PG4.1, IPA.3 No protein-ligand interaction detected (PLIP) IPA.5: 4 residues within 4Å: Chain A: K.71, Q.98, F.100, D.103 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.100, A:F.100 Hydrogen bonds: A:K.71 IPA.8: 3 residues within 4Å: Ligands: PG4.6, FLC.7, IPA.9 No protein-ligand interaction detected (PLIP) IPA.9: 2 residues within 4Å: Ligands: PG4.6, IPA.8 No protein-ligand interaction detected (PLIP) IPA.10: 4 residues within 4Å: Chain B: K.71, Q.98, F.100, D.103 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.100, B:F.100 Hydrogen bonds: B:K.71 IPA.13: 3 residues within 4Å: Ligands: PG4.11, FLC.12, IPA.14 No protein-ligand interaction detected (PLIP) IPA.14: 2 residues within 4Å: Ligands: PG4.11, IPA.13 No protein-ligand interaction detected (PLIP) IPA.15: 4 residues within 4Å: Chain C: K.71, Q.98, F.100, D.103 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.100, C:F.100 Hydrogen bonds: C:K.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miao, H. et al., Structural insights into the C1q domain of Caprin-2 in canonical Wnt signaling. J.Biol.Chem. (2014)

Release Date

2014-10-29

Peptides

Caprin-2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Caprin-2