SMTL ID : 7yxb.1 (1 other biounit)

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: 6 residues within 4Å: Chain A: V.116, N.118, E.166, H.167, W.168 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.166, A:W.168 EDO.2: 1 residues within 4Å: Chain A: D.142 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.142 Water bridges: A:R.140, A:D.142, A:D.142 EDO.3: 2 residues within 4Å: Chain A: H.33, D.35 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: N.118 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.1, B:D.1 EDO.5: 4 residues within 4Å: Chain A: E.3, E.4, H.5, D.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.3, A:E.3 EDO.6: 5 residues within 4Å: Chain B: E.21, R.22, V.23, V.74, R.79 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.23, B:R.79, B:R.79 Water bridges: B:D.75, B:D.75 EDO.7: 4 residues within 4Å: Chain B: S.125, E.175, H.176, P.177 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.176 EDO.8: 3 residues within 4Å: Chain B: Y.95, L.179, L.183 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain B: F.131, T.171, T.184 No protein-ligand interaction detected (PLIP)

1 x FLC: CITRATE ANION(Non-covalent)

FLC.10: 8 residues within 4Å: Chain B: Q.69, K.70, A.73, T.76, Y.77 Chain C: M.10, A.11, T.12 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:T.12, C:T.12 Water bridges: B:Q.69, B:T.76 Salt bridges: B:K.70, B:K.70

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

2023-02-22

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen DR beta chain: B
CLIP peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen DR beta chain

CLIP peptide

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