SMTL ID : 7ytc.1

Cryo-EM structure of human FcmR bound to IgM-Fc/J

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.219 Chain I: T.58 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.219 NAG.2: 6 residues within 4Å: Chain A: L.217, N.219 Chain B: N.219, S.221 Ligands: NAG.1, NAG.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.221, B:S.221 Hydrophobic interactions: A:L.217 NAG.3: 4 residues within 4Å: Chain B: L.217 Chain C: N.219 Ligands: NAG.2, NAG.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.217 NAG.4: 4 residues within 4Å: Chain D: N.219, S.221 Ligands: NAG.3, NAG.5 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.219 NAG.5: 3 residues within 4Å: Chain E: N.219, S.221 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain F: N.219, V.220 Ligands: NAG.7 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain F: S.221 Chain G: N.219, S.221 Ligands: NAG.6, NAG.8 No protein-ligand interaction detected (PLIP) NAG.8: 5 residues within 4Å: Chain H: N.219, S.221 Chain J: N.219 Ligands: NAG.7, NAG.10 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.219 NAG.9: 2 residues within 4Å: Chain I: N.48, D.51 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.51 NAG.10: 5 residues within 4Å: Chain J: N.219, S.221 Chain K: N.219 Ligands: NAG.8, NAG.11 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:S.221, K:N.219 NAG.11: 7 residues within 4Å: Chain I: R.20, I.22, E.34 Chain K: L.217, N.219, S.221 Ligands: NAG.10 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain I Hydrogen bonds: K:N.219, I:R.20, I:R.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Immunoglobulin M perception by Fc mu R. Nature (2023)

Release Date

2023-02-01

Peptides

Immunoglobulin heavy constant mu: ABCDEFGHJK
Immunoglobulin J chain: I
Fas apoptotic inhibitory molecule 3: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

J
K

K
L

I
J

L
R

Immunoglobulin heavy constant mu

Immunoglobulin J chain

Fas apoptotic inhibitory molecule 3

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