SMTL ID : 6kxs.1

Cryo-EM structure of human IgM-Fc in complex with the J chain and the ectodomain of pIgR

Coordinates

PDB Format

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 K: N.48, D.51 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: N.370 Chain K: T.58 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.58 NAG.3: 6 residues within 4Å: Chain A: L.368, N.370 Chain B: N.370, S.372 Ligands: NAG.2, NAG.4 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.368 Hydrogen bonds: B:N.370, B:S.372, B:S.372 NAG.4: 4 residues within 4Å: Chain C: N.370, S.372 Ligands: NAG.3, NAG.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.372, C:S.372 NAG.5: 4 residues within 4Å: Chain D: N.370, S.372 Ligands: NAG.4, NAG.6 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.370, D:S.372, D:S.372 NAG.6: 4 residues within 4Å: Chain D: T.367 Chain E: N.370, S.372 Ligands: NAG.5 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:T.367 Hydrogen bonds: E:N.370, E:S.372, E:S.372 NAG.7: 5 residues within 4Å: Chain F: K.365, N.370, V.371, S.372 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.372 NAG.8: 4 residues within 4Å: Chain G: N.370, S.372 Ligands: NAG.7, NAG.9 No protein-ligand interaction detected (PLIP) NAG.9: 6 residues within 4Å: Chain H: N.370, S.372 Chain I: L.368, N.370 Ligands: NAG.8, NAG.10 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.370 NAG.10: 5 residues within 4Å: Chain I: N.370, S.372 Chain J: N.370 Ligands: NAG.9, NAG.11 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:S.372, J:N.370 NAG.11: 7 residues within 4Å: Chain J: L.368, N.370, S.372 Chain K: R.20, I.22, N.36 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.20, K:N.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structural insights into immunoglobulin M. Science (2020)

Release Date

2020-02-05

Peptides

Immunoglobulin heavy constant mu: ABCDEFGHIJ
Immunoglobulin J chain: K
Polymeric immunoglobulin receptor: 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

I
K

J
L

K
J

L
P

Immunoglobulin heavy constant mu

Immunoglobulin J chain

Polymeric immunoglobulin receptor

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