SMTL ID : 9bde.1

Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain B: N.3336, F.3357, N.3358, Q.3359 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.3358, B:N.3358, B:Q.3359, B:Q.3359 NAG.2: 3 residues within 4Å: Chain B: N.2779, G.2780, G.2788 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.2788 NAG.3: 3 residues within 4Å: Chain B: N.3101, S.3103, H.3114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.3088, B:N.3101, B:S.3103, B:S.3103 NAG.4: 5 residues within 4Å: Chain B: A.3396, T.3397, A.3398, S.3409, N.3411 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.3396, B:A.3398 Hydrogen bonds: B:S.3409, B:N.3411 NAG.5: 4 residues within 4Å: Chain B: N.3465, S.3467, Y.3470, T.3472 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.3467

7 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain F: W.87, D.90, Q.92, D.94, D.100, E.101 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:W.87, F:D.90, F:Q.92, F:D.94, F:E.101 CA.7: 6 residues within 4Å: Chain F: F.126, C.128, D.129, D.131, D.139, E.140 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:F.126, F:D.129, F:D.139, F:D.139, F:E.140 CA.8: 7 residues within 4Å: Chain F: Q.163, L.164, W.165, A.166, C.167, D.168, D.170 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:Q.163, F:L.164, F:W.165, F:A.166, F:D.170 CA.9: 6 residues within 4Å: Chain F: W.214, D.217, G.219, P.220, D.227, E.228 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:W.214, F:D.217, F:G.219, F:D.227 CA.10: 7 residues within 4Å: Chain F: R.253, Q.254, C.255, D.256, R.257, D.266, E.267 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.256, F:E.267 CA.11: 5 residues within 4Å: Chain F: K.294, N.297, A.299, D.301, E.308 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.301, F:E.308 CA.12: 8 residues within 4Å: Chain F: G.314, T.315, N.316, D.331, L.332, K.333, I.334, G.335 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.331, F:D.331, F:L.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reimund, M. et al., Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor. Nature (2024)

Release Date

2024-12-25

Peptides

Legobody 8D3 Fab Heavy Chain: A
Apolipoprotein B 100: B
Legobody 8D3 Fab light chain: C
Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G: D
ApoB100 nanobody 4: E
Low-density lipoprotein receptor: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
L

D
B

E
N

F
R

Legobody 8D3 Fab Heavy Chain

Apolipoprotein B 100

Legobody 8D3 Fab light chain

Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

ApoB100 nanobody 4

Low-density lipoprotein receptor

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