SMTL ID : 8wys.1

Local map of human CD5L bound to IgM-Fc/J

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-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: 3 residues within 4Å: Chain D: N.71, S.73, D.74 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: N.390, S.392 Chain D: T.81, R.82 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.390, D:T.81 NAG.3: 4 residues within 4Å: Chain B: N.390, S.392 Chain D: E.57, N.59 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain C: D.282, D.283, E.351 Chain D: N.129 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:D.282, C:D.283, C:E.351, C:E.351, D:N.129 CA.5: 3 residues within 4Å: Chain C: D.283, D.323, D.346 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.283, C:D.323, C:D.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., CD5L associates with IgM via the J chain. Nat Commun (2024)

Release Date

2024-10-09

Peptides

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu: AB
Interleukin-2,CD5 antigen-like: C
Immunoglobulin J chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
M

D
J

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

Interleukin-2,CD5 antigen-like

Immunoglobulin J chain

Related Entries With Identical Sequence