SMTL ID : 2fcw.2 (1 other biounit)

Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

hetero-2-2-mer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: E.51, E.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.51, A:E.55 NA.2: 4 residues within 4Å: Chain A: I.10, D.14 Chain C: S.18, R.105 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.14, C:R.105, C:R.105 NA.3: 1 residues within 4Å: Chain A: L.26 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.17, A:D.23, A:D.23 NA.8: 3 residues within 4Å: Chain B: K.1, G.13, C.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.1, B:K.1 NA.12: 2 residues within 4Å: Chain C: E.51, E.55 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.51 NA.13: 4 residues within 4Å: Chain A: S.18, R.105 Chain C: I.10, D.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.105, A:R.105, C:D.14 NA.14: 1 residues within 4Å: Chain C: L.26 No protein-ligand interaction detected (PLIP) NA.19: 3 residues within 4Å: Chain D: K.1, G.13, C.15 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.1 Water bridges: D:K.1

10 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 8 residues within 4Å: Chain A: H.45, Y.46, L.79 Chain B: S.24, T.53, W.59, D.66, E.68 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.59, A:Y.46, A:L.79 Hydrogen bonds: B:S.24, B:D.66, B:E.68, A:H.45 MPD.5: 4 residues within 4Å: Chain A: E.3, F.4, R.30, K.34 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.3, A:K.34 Hydrogen bonds: A:E.3, A:R.30, A:R.30 Water bridges: A:E.37 MPD.9: 3 residues within 4Å: Chain B: E.73, W.74, P.75 No protein-ligand interaction detected (PLIP) MPD.10: 5 residues within 4Å: Chain B: Q.48, C.49, N.50, S.52, R.77 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.50 Hydrogen bonds: B:R.77 Water bridges: B:Q.48, B:R.77 MPD.11: 4 residues within 4Å: Chain B: T.2, C.3, S.4, Q.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.2 Hydrogen bonds: B:C.3 MPD.15: 8 residues within 4Å: Chain C: H.45, Y.46, L.79 Chain D: S.24, T.53, W.59, D.66, E.68 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.59, C:Y.46, C:L.79 Hydrogen bonds: D:S.24, D:D.66, D:E.68, C:H.45 MPD.16: 4 residues within 4Å: Chain C: E.3, F.4, R.30, K.34 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:E.3, C:K.34 Hydrogen bonds: C:E.3, C:R.30, C:R.30 MPD.20: 3 residues within 4Å: Chain D: E.73, W.74, P.75 No protein-ligand interaction detected (PLIP) MPD.21: 5 residues within 4Å: Chain D: Q.48, C.49, N.50, S.52, R.77 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:N.50 Water bridges: D:Q.48, D:R.77 MPD.22: 4 residues within 4Å: Chain D: T.2, C.3, S.4, Q.5 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.2 Hydrogen bonds: D:C.3

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain B: F.20, D.23, D.25, D.27, D.33, E.34 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:F.20, B:D.23, B:D.25, B:D.27, B:D.33, B:E.34 CA.7: 6 residues within 4Å: Chain B: W.59, D.62, D.64, D.66, D.72, E.73 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.59, B:D.62, B:D.64, B:D.66, B:D.72, B:E.73 CA.17: 6 residues within 4Å: Chain D: F.20, D.23, D.25, D.27, D.33, E.34 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:F.20, D:D.23, D:D.25, D:D.27, D:D.33, D:E.34 CA.18: 6 residues within 4Å: Chain D: W.59, D.62, D.64, D.66, D.72, E.73 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:W.59, D:D.62, D:D.64, D:D.66, D:D.72, D:E.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fisher, C. et al., Structure of an LDLR-RAP Complex Reveals a General Mode for Ligand Recognition by Lipoprotein Receptors. Mol.Cell (2006)

Release Date

2006-05-16

Peptides

Alpha-2-macroglobulin receptor-associated protein: AC
Low-density lipoprotein receptor: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Alpha-2-macroglobulin receptor-associated protein

Low-density lipoprotein receptor

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