SMTL ID : 8bpe.1

8:1 binding of FcMR on IgM pentameric core

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-8-1-mer

Ligands

3 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: 3 residues within 4Å: Chain D: S.38 Chain G: N.335 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.38 NAG-NAG.2: 3 residues within 4Å: Chain F: S.38 Chain I: N.335, S.337 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain R: N.71, D.74 No protein-ligand interaction detected (PLIP)

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

NAG.4: 5 residues within 4Å: Chain A: N.335, S.337 Chain O: N.335 Ligands: NAG.7, NAG.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.335, A:S.337, A:S.337 NAG.5: 5 residues within 4Å: Chain B: N.335, S.337 Chain C: N.335 Ligands: NAG.6, NAG.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.335, B:S.337, B:S.337 NAG.6: 3 residues within 4Å: Chain C: N.335 Ligands: NAG.5, NAG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.335 NAG.7: 4 residues within 4Å: Chain A: N.335 Chain E: N.335, S.337 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.335, E:S.337, E:S.337 NAG.8: 4 residues within 4Å: Chain H: N.335, S.337 Ligands: NAG-NAG.1, NAG.5 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.337, H:S.337 NAG.9: 4 residues within 4Å: Chain O: N.335 Chain P: N.335 Ligands: NAG.4, NAG.10 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:N.335 NAG.10: 2 residues within 4Å: Chain P: N.335 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.335 NAG.11: 5 residues within 4Å: Chain R: E.57, N.59 Chain S: N.335, S.337 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S: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: ABCEGHIOPS
Fas apoptotic inhibitory molecule 3: DFJKLMNQ
Immunoglobulin J chain: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
K

E
D

G
F

H
G

I
E

O
B

P
A

S
L

D
M

F
P

J
O

K
R

L
N

M
Q

N
S

Q
I

R
J

Immunoglobulin heavy constant mu

Fas apoptotic inhibitory molecule 3

Immunoglobulin J chain

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