SMTL ID : 8jxj.1

rat megalin RAP complex leg

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

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: 11 residues within 4Å: Chain A: S.4054, P.4055, L.4057, N.4070, S.4072, S.4073, N.4124, F.4125, E.4126, Y.4407, G.4415 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: V.4035, L.4241, N.4329, S.4331, V.4332 No protein-ligand interaction detected (PLIP)

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-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain B: P.4055, L.4057, N.4070, S.4072, S.4073, E.4126, H.4387, E.4413, V.4414, G.4415 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.4126, B:E.4126

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 6 residues within 4Å: Chain B: V.4035, D.4036, L.4241, N.4329, S.4331, V.4332 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.3980, R.3994 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.3994 NAG.10: 2 residues within 4Å: Chain B: N.3980, R.3994 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.3994

8 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: W.45, D.48, T.50, D.52, D.58, E.59 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.45, A:D.48, A:T.50, A:D.52, A:D.58 CA.7: 8 residues within 4Å: Chain A: W.85, C.87, D.88, E.89, D.90, D.92, E.99 Chain B: K.4027 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.85, A:D.90, A:D.92, A:E.99, A:E.99 CA.8: 6 residues within 4Å: Chain A: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.3947, A:D.3950, A:V.3952, A:D.3954, A:E.3961 CA.9: 7 residues within 4Å: Chain A: D.4009, I.4010, E.4012, N.4025, S.4026, G.4028, S.4029 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.4009, A:E.4012, A:E.4012, A:S.4026, A:S.4029 CA.11: 7 residues within 4Å: Chain B: W.45, C.47, D.48, T.50, D.52, D.58, E.59 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.48, B:T.50, B:D.52, B:D.58, B:E.59 CA.12: 6 residues within 4Å: Chain B: W.85, D.88, D.90, D.92, D.98, E.99 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.85, B:D.88, B:D.90, B:D.98, B:E.99 CA.13: 6 residues within 4Å: Chain B: Y.3947, D.3950, V.3952, D.3954, D.3960, E.3961 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Y.3947, B:D.3950, B:V.3952, B:D.3960, B:E.3961 CA.14: 7 residues within 4Å: Chain B: D.4009, I.4010, E.4012, N.4025, S.4026, G.4028, S.4029 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.4009, B:I.4010, B:E.4012, B:E.4012, B:S.4026

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, S. et al., Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-06-19

Peptides

LDL receptor related protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LDL receptor related protein 2

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