SMTL ID : 3v64.1

Crystal Structure of agrin and LRP4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.101, N.103, S.105 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.103 Hydrogen bonds: A:N.101, A:N.103, A:S.105 NAG.2: 2 residues within 4Å: Chain A: N.324, Y.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.324

5 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: N.311, G.312, C.314, Y.325 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain B: D.63, L.80, Q.130, D.132 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.63, B:L.80, B:Q.130, B:D.132 CA.8: 4 residues within 4Å: Chain C: D.63, L.80, Q.130, D.132 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.63, C:L.80, C:Q.130 CA.10: 5 residues within 4Å: Chain D: C.307, N.311, G.313, C.314, C.318 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:N.311, H2O.5 CA.11: 3 residues within 4Å: Chain D: V.92, D.95, E.116 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:V.92, D:D.95, D:E.116

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: A.148, H.149, P.330, F.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.149 Salt bridges: A:H.149 PO4.5: 6 residues within 4Å: Chain A: R.83, W.125, V.126, P.301, A.302, G.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.125, A:G.303 PO4.7: 7 residues within 4Å: Chain B: N.17, N.37, H.38, I.55, L.137, V.168, G.169 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.17, B:N.17, B:N.17, B:H.38, B:G.169 PO4.9: 6 residues within 4Å: Chain C: S.36, N.37, H.38, F.39, V.168, G.169 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.36, C:H.38, C:H.38, C:G.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zong, Y. et al., Structural basis of agrin-LRP4-MuSK signaling. Genes Dev. (2012)

Release Date

2012-04-25

Peptides

Low-density lipoprotein receptor-related protein 4: AD
agrin: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
D

B
A

C
B

Low-density lipoprotein receptor-related protein 4

agrin

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