SMTL ID : 9cwm.1

Cryo-EM structure of human Low-density lipoprotein receptor-related protein 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

9 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.1: 6 residues within 4Å: Chain A: S.2105, S.2106, F.2108, K.2128, I.2176, N.2177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.2128, A:K.2128 NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: I.3197, E.3198, Y.3200, N.3211, I.3222, L.3256 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.3198 Hydrogen bonds: A:E.3198 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: E.3238, K.3239, F.3255, N.3257, T.3259 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: Y.3334, R.3348, N.3355, S.3357, E.3395, H.3397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.3393, A:D.3393, A:E.3395, A:E.3395 NAG-NAG-BMA.7: 6 residues within 4Å: Chain B: S.2105, S.2106, F.2108, K.2128, I.2176, N.2177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.2105 NAG-NAG-BMA.8: 6 residues within 4Å: Chain B: I.3197, E.3198, Y.3200, N.3211, I.3222, L.3256 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.3198 Hydrogen bonds: B:E.3198 NAG-NAG-BMA.9: 5 residues within 4Å: Chain B: E.3238, K.3239, F.3255, N.3257, T.3259 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 7 residues within 4Å: Chain B: Y.3334, R.3348, N.3355, S.3357, D.3393, E.3395, H.3397 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.3393, B:D.3393, B:E.3395, B:E.3395 NAG-NAG-BMA.12: 7 residues within 4Å: Chain B: H.4020, A.4033, D.4034, Y.4238, L.4239, N.4327, S.4329 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.4329, B:S.4329

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG.5: 4 residues within 4Å: Chain A: D.4034, N.4327, S.4329, V.4330 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: S.4053, L.4055, N.4068, S.4071, N.4122, F.4123, E.4124 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain B: S.4052, S.4053, L.4055, N.4068, S.4071, E.4124 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: E.460, N.463 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: L.862, P.863, N.866, P.1254 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: F.1494, N.1496, T.1498 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: K.1549, N.1550, R.1589 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: H.1672, N.1675 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: K.1805, N.1810 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: F.2219, N.2224, T.2226 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: S.2498, N.2499, H.2664, I.2665 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: H.3124, N.3125 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.3315 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.3446 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: I.378, N.388, S.390 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: G.376, I.378, N.388, S.390 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: K.447, E.460, N.463 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: L.862, P.863, N.866, P.1254 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: F.1494, N.1496, T.1498 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: K.1549, N.1550, R.1589 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: H.1672, N.1675 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: F.2219, N.2224, T.2226 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: S.2498, N.2499 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: H.3124, N.3125 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: A.3314, N.3315 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.3446 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Cryo-EM structure of human Low-density lipoprotein receptor-related protein 2. To Be Published

Release Date

2025-08-06

Peptides

Low-density lipoprotein receptor-related protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Low-density lipoprotein receptor-related protein 2