SMTL ID : 9bdt.1

Apolipoprotein B 100 bound to LDL receptor and legobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-2-1-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: Q.3088, N.3101, F.3102, S.3103, H.3114 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: F.3357, N.3358, Q.3359, D.3361 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.3357 Hydrogen bonds: A:N.3358 NAG.3: 3 residues within 4Å: Chain A: F.178, L.179, N.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.178 NAG.4: 4 residues within 4Å: Chain A: N.3465, S.3466, S.3467, T.3472 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.3472 Hydrogen bonds: A:N.3465, A:S.3466 NAG.5: 6 residues within 4Å: Chain A: A.3398, L.3399, S.3400, S.3409, H.3410, N.3411 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.3398 Hydrogen bonds: A:S.3409, A:S.3409, A:S.3409, A:H.3410

7 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain G: W.87, D.90, Q.92, D.94, E.101 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.90, G:D.90, G:Q.92, G:D.94, G:E.101 CA.7: 6 residues within 4Å: Chain G: F.126, C.128, D.129, D.131, D.139, E.140 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:F.126, G:D.129, G:D.139, G:D.139, G:E.140 CA.8: 5 residues within 4Å: Chain G: W.165, A.166, C.167, D.168, D.170 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:W.165, G:A.166, G:D.168, G:D.170 CA.9: 7 residues within 4Å: Chain A: R.3391 Chain G: W.214, D.217, G.219, D.221, D.227, E.228 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:W.214, G:D.217, G:D.217, G:G.219, G:D.227 CA.10: 6 residues within 4Å: Chain G: R.253, Q.254, C.255, D.256, D.266, E.267 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.256, G:D.266, G:D.266, G:E.267 CA.11: 7 residues within 4Å: Chain G: G.314, T.315, N.316, E.317, D.331, L.332, K.333 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:G.314, G:D.331, G:L.332 CA.12: 6 residues within 4Å: Chain G: K.294, V.295, N.297, D.301, D.307, E.308 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:K.294, G:D.301, G:D.307, G:E.308

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

Apolipoprotein B-100: A
Legobody 8D3 Fab Heavy Chain: B
Legobody 8D3 Fab Light Chain: C
Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G: D
Low-density lipoprotein receptor: EG
ApoB100 nanobody 4: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

D
B

E
I

G
R

F
N

Apolipoprotein B-100

Legobody 8D3 Fab Heavy Chain

Legobody 8D3 Fab Light Chain

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Low-density lipoprotein receptor

ApoB100 nanobody 4

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