SMTL ID : 8bpf.1

FcMR binding at subunit Fcu1 of IgM pentamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-1-1-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: 2 residues within 4Å: Chain J: N.71, D.74 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.335 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.335 NAG.3: 5 residues within 4Å: Chain A: L.333, N.335 Chain B: N.335 Ligands: NAG.2, NAG.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.333 Hydrogen bonds: A:N.335, B:N.335 NAG.4: 5 residues within 4Å: Chain B: N.335 Chain C: N.335, S.337 Ligands: NAG.3, NAG.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.335, C:S.337, C:S.337 NAG.5: 4 residues within 4Å: Chain C: N.335 Chain D: N.335, S.337 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.335, D:S.337, D:S.337 NAG.6: 2 residues within 4Å: Chain E: N.335, S.337 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.337 NAG.7: 3 residues within 4Å: Chain F: N.335, S.337 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.335, F:S.337 NAG.8: 5 residues within 4Å: Chain F: S.337 Chain G: N.335, S.337 Ligands: NAG.7, NAG.9 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:S.337, G:S.337, G:S.337 NAG.9: 5 residues within 4Å: Chain H: N.335, S.337 Chain K: N.335 Ligands: NAG.8, NAG.10 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:N.335, H:S.337, H:S.337 NAG.10: 4 residues within 4Å: Chain K: N.335 Chain L: L.333 Ligands: NAG.9, NAG.11 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.335 NAG.11: 4 residues within 4Å: Chain J: E.57, N.59 Chain L: N.335 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Q. et al., Structural basis for Fc receptor recognition of immunoglobulin M. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-04-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

K
K

L
L

I
I

J
J

Immunoglobulin heavy constant mu

Fas apoptotic inhibitory molecule 3

Immunoglobulin J chain

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