SMTL ID : 8vdu.1

Crystal structure of hybrid insulin peptide (InsC8-15-IAPP74-80) bound to HLA-DQ8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-4-4-4-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: N.81 Chain H: R.23, D.43 Chain K: L.85 Chain L: Q.2 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain L Hydrogen bonds: H:D.43, L:Q.2, L:Q.2

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

NAG.2: 5 residues within 4Å: Chain A: Y.19, V.119, N.121, E.169, W.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.169, A:W.171 NAG.4: 2 residues within 4Å: Chain H: N.19, E.22 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:E.22 NAG.5: 4 residues within 4Å: Chain J: N.121, E.169, H.170, W.171 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:E.169

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: S.18, Y.19, G.20 Chain K: R.94, P.178 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.94 PEG.6: 4 residues within 4Å: Chain A: S.18 Chain K: Q.92, R.94 Ligands: PEG.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, M.T. et al., A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8. J.Biol.Chem. (2024)

Release Date

2024-08-07

Peptides

MHC class II HLA-DQ-alpha chain: ADGJ
MHC class II HLA-DQ-beta-1: BEHK
Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80): CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

B
B

E
E

H
H

K
K

C
C

F
F

I
I

L
L

MHC class II HLA-DQ-alpha chain

MHC class II HLA-DQ-beta-1

Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80)

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