SMTL ID : 7ysg.1

Cryo-EM structure of human FcmR bound to sIgM

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-1-1-4-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: 2 residues within 4Å: Chain I: N.48, D.51 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.219, S.221 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.221 NAG.3: 6 residues within 4Å: Chain A: L.217, N.219 Chain B: N.219, S.221 Ligands: NAG.2, NAG.4 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.217 Hydrogen bonds: B:N.219, B:S.221, B:S.221 NAG.4: 5 residues within 4Å: Chain B: N.219 Chain C: N.219, S.221 Ligands: NAG.3, NAG.5 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain D: N.219, S.221 Chain E: S.221 Ligands: NAG.4, NAG.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.219 NAG.6: 4 residues within 4Å: Chain D: N.219 Chain E: N.219, S.221 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain F: K.214, N.219, V.220, S.221 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.214, F:S.221 NAG.8: 5 residues within 4Å: Chain F: S.221 Chain G: N.219, S.221 Chain H: N.219 Ligands: NAG.9 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 1 interactions with chain F Hydrogen bonds: G:N.219, G:S.221, H:N.219, F:S.221 NAG.9: 4 residues within 4Å: Chain G: S.221 Chain H: N.219 Ligands: NAG.8, NAG.10 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:N.219, G:S.221 NAG.10: 5 residues within 4Å: Chain J: N.219, S.221 Chain K: N.219 Ligands: NAG.9, NAG.11 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:N.219, J:N.219, J:S.221 NAG.11: 8 residues within 4Å: Chain I: R.4, R.20, I.22, E.34, N.36 Chain K: N.219, S.221 Ligands: NAG.10 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:R.4, I:R.20, I:R.20, I:N.36

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
Secretory component: L
Fas apoptotic inhibitory molecule 3: MNOP

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
P

M
R

N
S

O
U

P
V

Immunoglobulin heavy constant mu

Immunoglobulin J chain

Secretory component

Fas apoptotic inhibitory molecule 3

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