SMTL ID : 1n7d.1

Extracellular domain of the LDL receptor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA-MAN-MAN.1: 6 residues within 4Å: Chain A: F.132, Q.133, C.134, N.135, G.155, Q.161 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 3 residues within 4Å: Chain A: N.251, V.252, T.253 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: T.294, N.295, E.296, D.310, L.311, K.312, I.313, Y.315 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.294, A:E.296, A:D.310, A:L.311 CA.4: 6 residues within 4Å: Chain A: D.333, I.334, D.335, E.336, N.349, L.350 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.333, A:D.333, A:I.334, A:E.336, A:L.350 CA.5: 7 residues within 4Å: Chain A: W.193, D.196, G.198, D.200, D.206, E.207, K.582 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.196, A:G.198, A:D.200, A:D.206, A:E.207 CA.6: 8 residues within 4Å: Chain A: R.232, Q.233, C.234, D.235, E.237, D.239, D.245, E.246 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:R.232, A:Q.233, A:D.245, A:E.246, A:E.246 CA.7: 6 residues within 4Å: Chain A: K.273, N.276, A.278, D.280, D.286, E.287 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:K.273, A:D.280, A:D.286, A:E.287 CA.8: 7 residues within 4Å: Chain A: W.144, D.147, D.149, P.150, D.151, D.157, E.158 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.147, A:D.147, A:D.149, A:D.151, A:D.157 CA.9: 6 residues within 4Å: Chain A: F.105, D.108, D.110, D.112, D.118, E.119 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.108, A:D.112, A:D.118 CA.10: 6 residues within 4Å: Chain A: W.66, D.69, Q.71, D.73, D.79, E.80 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.66, A:D.69, A:Q.71, A:D.79, A:D.79

3 x KEG: 12-TUNGSTOPHOSPHATE(Non-covalent)

KEG.11: 3 residues within 4Å: Chain A: G.55, G.56, N.76 0 PLIP interactions: KEG.12: 4 residues within 4Å: Chain A: R.103, Q.104, S.449, R.450 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.103, A:Q.104, A:S.449 Metal complexes: KEG.12 KEG.13: 2 residues within 4Å: Chain A: R.406, N.407 0 PLIP interactions:

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudenko, G. et al., Structure of the LDL receptor extracellular domain at endosomal pH. Science (2002)

Release Date

2003-01-21

Peptides

Low-density lipoprotein receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Low-density lipoprotein receptor