SMTL ID : 8wyr.1

Cryo-EM structure of human CD5L bound to IgM-Fc/J

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: 3 residues within 4Å: Chain I: N.71, S.73, D.74 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: L.388, N.390 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.388 NAG.3: 6 residues within 4Å: Chain A: L.388, N.390 Chain B: N.390, S.392 Ligands: NAG.2, NAG.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.390, B:S.392 NAG.4: 7 residues within 4Å: Chain B: L.388, N.390 Chain C: N.390, S.392 Chain D: S.392 Ligands: NAG.3, NAG.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.388 Hydrogen bonds: C:S.392, C:S.392 NAG.5: 5 residues within 4Å: Chain C: N.390 Chain D: N.390 Chain E: S.392 Ligands: NAG.4, NAG.6 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: C:N.390, D:N.390, E:S.392 NAG.6: 4 residues within 4Å: Chain D: T.387, N.390 Chain E: N.390 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.390 NAG.7: 6 residues within 4Å: Chain F: K.385, N.390, V.391, S.392 Chain G: N.390 Ligands: NAG.8 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.385, F:S.392 NAG.8: 5 residues within 4Å: Chain F: S.392 Chain G: N.390, S.392 Chain H: L.388 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.392 NAG.9: 6 residues within 4Å: Chain G: S.392 Chain H: N.390, S.392 Chain J: L.388, N.390 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.390 NAG.10: 5 residues within 4Å: Chain J: N.390, S.392 Chain K: N.390 Ligands: NAG.9, NAG.11 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:S.392, K:N.390 NAG.11: 9 residues within 4Å: Chain I: R.27, R.43, E.57, N.59, I.60, R.61 Chain K: N.390, S.392 Ligands: NAG.10 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain K Hydrophobic interactions: I:R.61 Hydrogen bonds: I:R.27, I:R.43, K:N.390, K:S.392

2 x CA: CALCIUM ION(Non-covalent)

CA.12: 4 residues within 4Å: Chain I: N.129 Chain L: D.282, D.283, E.351 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain I Metal complexes: L:D.282, L:E.351, L:E.351, I:N.129 CA.13: 4 residues within 4Å: Chain L: D.283, D.323, N.324, D.346 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.283, L:D.323

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: ABCDEFGHJK
Immunoglobulin J chain: I
Interleukin-2,CD5 antigen-like: 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

J
K

K
L

I
J

L
M

Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu

Immunoglobulin J chain

Interleukin-2,CD5 antigen-like

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