SMTL ID : 7tuc.1

Crystal structure of HLA-B*44:05 (T73C) with 9mer EEFGRAFSF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU- GLU- PHE- GLY- ARG- ALA- PHE- SER- PHE: MHC class II antigen peptide(Non-covalent)

GLU-GLU-PHE-GLY-ARG-ALA-PHE-SER-PHE.1: 30 residues within 4Å: Chain A: M.5, Y.7, Y.9, T.24, K.45, Y.59, R.62, E.63, I.66, S.67, N.70, C.73, N.77, T.80, Y.84, I.95, Y.99, Y.116, Y.123, T.143, K.146, W.147, V.152, Q.155, D.156, Y.159, L.163, S.167, R.170, Y.171 39 PLIP interactions: 39 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:I.95, A:I.95, A:Y.116, A:Y.123, A:V.152, A:V.152, A:Y.159, A:Y.159, A:Y.159 Hydrogen bonds: A:Y.7, A:E.63, A:N.77, A:Y.99, A:Y.99, A:Y.99, A:T.143, A:Q.155, A:Y.159, A:S.167, A:Y.171 Water bridges: A:Y.9, A:T.24, A:T.24, A:R.62, A:R.62, A:R.62, A:Y.74, A:T.80, A:R.97, A:R.97, A:W.147, A:Q.155, A:R.170 Salt bridges: A:K.45, A:R.62, A:K.146, A:R.170

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: H.3, D.29, L.179, Q.180, R.181, A.182, Y.209, P.210, E.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.29, A:R.181 Water bridges: A:G.1, A:Q.180, A:Y.209 GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.64 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.30, B:Y.64 Water bridges: A:R.6, B:Y.64

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

EDO.4: 3 residues within 4Å: Chain A: S.92, H.93, D.119 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.93 Water bridges: A:Q.87, A:H.93, A:D.119, B:I.2, B:H.32 EDO.5: 8 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.234, B:S.12, B:M.100 Water bridges: A:Q.242, B:R.13 EDO.6: 6 residues within 4Å: Chain B: V.10, V.94, K.95, W.96, D.97, M.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.95, B:D.97, B:M.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, J. et al., Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation. Nat Commun (2022)

Release Date

2022-09-07

Peptides

HLA class I histocompatibility antigen, B alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I histocompatibility antigen, B alpha chain

Beta-2-microglobulin

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