SMTL ID : 8r83.1

pentameric IgMFc-AIM complex global refinement

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-10-1-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 L: N.71, S.73 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.251, D.252, E.320 Chain L: N.129 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain L Metal complexes: A:D.251, A:D.252, A:E.320, L:N.129 CA.3: 4 residues within 4Å: Chain A: D.252, D.292, N.293, D.315 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.252, A:D.292, A:D.315

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

NAG.4: 4 residues within 4Å: Chain B: N.348 Chain K: L.346, N.348 Ligands: NAG.5 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain B Hydrophobic interactions: K:L.346 Hydrogen bonds: B:N.348 NAG.5: 4 residues within 4Å: Chain B: L.346 Chain C: N.348 Ligands: NAG.4, NAG.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.346 Hydrogen bonds: C:N.348 NAG.6: 4 residues within 4Å: Chain D: N.348, S.350 Chain I: S.350 Ligands: NAG.5 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain I Hydrogen bonds: D:N.348, D:S.350, I:S.350 NAG.7: 4 residues within 4Å: Chain E: L.346, N.348 Chain F: N.348 Ligands: NAG.8 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:L.346 Hydrogen bonds: E:N.348, F:N.348 NAG.8: 5 residues within 4Å: Chain F: L.346, N.348 Chain G: N.348 Ligands: NAG.7, NAG.9 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:N.348 Hydrophobic interactions: F:L.346 NAG.9: 3 residues within 4Å: Chain H: N.348, S.350 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.348, H:S.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Q. et al., Cryo-EM reveals structural basis for human AIM/CD5L recognition of polymeric immunoglobulin M. Nat Commun (2024)

Release Date

2024-11-06

Peptides

CD5 antigen-like: A
Ig-like domain-containing protein: BCDEFGHIJK
Immunoglobulin J chain: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
B

C
C

D
D

E
L

F
K

G
H

H
G

I
E

J
F

K
A

L
J

CD5 antigen-like

Ig-like domain-containing protein

Immunoglobulin J chain

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