SMTL ID : 7z0q.1

MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: H.33, R.44, E.134, T.135 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.30, A:E.30 EDO.2: 3 residues within 4Å: Chain A: N.118, E.166, W.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.168 EDO.3: 6 residues within 4Å: Chain A: G.49, R.50, F.51, A.52, S.53 Chain C: S.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.50 EDO.4: 4 residues within 4Å: Chain A: H.33, E.134, T.135, V.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.134, A:E.134 Water bridges: A:T.135, A:V.136 EDO.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: I.8, D.25, G.28, P.139, R.140, E.141, R.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.25, A:R.140, A:R.146 Water bridges: A:R.146 EDO.7: 8 residues within 4Å: Chain A: I.7, Q.9, F.24 Chain B: Y.12, C.14, V.77, N.81 Chain C: A.8 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:N.81, C:A.8, A:I.7 EDO.8: 2 residues within 4Å: Chain B: D.42, V.43 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain B: H.80 Chain C: S.3, K.4 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.3, C:K.4, B:H.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abualrous, E.T. et al., MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange. Nat.Chem.Biol. (2023)

Release Date

2023-03-08

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA-DRB1 protein: B
CLIP peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
G

HLA class II histocompatibility antigen, DR alpha chain

HLA-DRB1 protein

CLIP peptide

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