SMTL ID : 9coo.1

Nanobody 4 bound to Apolipoprotein B 100

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: G.3335, N.3336, F.3357, N.3358 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.3335, A:N.3336, A:N.3336 NAG.2: 5 residues within 4Å: Chain A: Q.3088, N.3101, F.3102, S.3103, H.3114 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.3114 Hydrogen bonds: A:Q.3088 NAG.3: 4 residues within 4Å: Chain A: F.3357, N.3358, V.3363 Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.3358

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain F: W.22, D.25, Q.27, D.29, D.35, E.36 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:W.22, F:D.25, F:Q.27, F:D.29, F:E.36 CA.5: 5 residues within 4Å: Chain F: F.61, D.64, D.66, D.68, E.75 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:F.61, F:D.64, F:D.66, F:E.75 CA.6: 7 residues within 4Å: Chain F: Q.98, L.99, W.100, A.101, C.102, D.103, D.105 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:L.99, F:W.100, F:D.103, F:D.105, F:D.105

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

E
N

F
R

Apolipoprotein B 100

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

Legobody 8D3 Fab Heavy Chain

Legobody 8D3 Fab Light Chain

ApoB100 nanobody 4

Low-density lipoprotein receptor

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