SMTL ID : 5trz.1

Crystal structure of MHC-I H2-KD complexed with peptides of Mycobacterial tuberculosis (YQSGLSIVM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-2-2-mer

Ligands

2 x TYR- GLN- SER- GLY- LEU- SER- ILE- VAL- MET: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YQSGLSIVM(Non-covalent)

TYR-GLN-SER-GLY-LEU-SER-ILE-VAL-MET.1: 27 residues within 4Å: Chain A: Y.6, V.8, F.21, A.23, F.44, Q.62, R.65, A.66, S.68, D.69, W.72, V.75, S.76, T.79, Y.83, F.94, R.96, F.98, I.141, T.142, K.145, W.146, A.149, D.151, Y.154, Y.155, Y.158 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:V.8, A:A.23, A:F.44, A:F.44, A:D.69, A:V.75, A:F.94, A:Y.154, A:Y.154 Hydrogen bonds: A:Y.6, A:Q.62, A:D.69, A:D.69, A:D.69, A:S.76, A:R.96, A:R.96, A:D.151, A:Y.154, A:Y.154, A:Y.155 Water bridges: A:Q.64, A:R.65, A:S.68, A:K.145, A:K.145, A:Y.154, A:Y.155 Salt bridges: A:K.145 pi-Stacking: A:Y.6, A:F.98 TYR-GLN-SER-GLY-LEU-SER-ILE-VAL-MET.2: 26 residues within 4Å: Chain C: Y.6, V.8, F.21, Q.62, R.65, S.68, D.69, W.72, V.75, S.76, T.79, Y.83, F.94, R.96, F.98, Y.122, A.138, T.142, K.145, W.146, A.149, D.151, Y.154, Y.155, Y.158 Ligands: EDO.10 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:R.65, C:D.69, C:W.72, C:V.75, C:F.94, C:Y.154, C:Y.158, C:Y.158 Hydrogen bonds: C:Y.6, C:Y.6, C:Q.62, C:R.65, C:D.69, C:D.69, C:D.69, C:D.69, C:S.76, C:T.79, C:R.96, C:R.96, C:K.145, C:D.151, C:D.151, C:Y.154, C:Y.155, C:Y.155, C:Y.158 Water bridges: C:K.145 Salt bridges: C:K.145 pi-Stacking: C:Y.6, C:F.98

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.7, Y.26, D.28, D.29 Chain B: Y.64 Ligands: GOL.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.29, B:Y.64 GOL.6: 3 residues within 4Å: Chain B: S.58, K.59 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.58, B:K.59 GOL.7: 5 residues within 4Å: Chain C: T.30, T.177, L.178, Y.208, G.238 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.30, C:T.30, C:T.177, C:D.237

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

EDO.4: 4 residues within 4Å: Chain A: V.230, E.231 Chain B: I.8, Q.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.231 EDO.5: 4 residues within 4Å: Chain A: Y.117, R.120, D.121, D.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.117 EDO.8: 5 residues within 4Å: Chain A: R.272 Chain C: E.172, L.173, N.175, E.176 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:L.173, C:N.175, C:E.176, A:R.272, A:R.272 EDO.9: 4 residues within 4Å: Chain C: H.261, H.262, L.265, P.268 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.262, C:L.265 EDO.10: 5 residues within 4Å: Chain C: A.149, G.150, E.153, Y.154 Ligands: TYR-GLN-SER-GLY-LEU-SER-ILE-VAL-MET.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.154 EDO.11: 2 residues within 4Å: Chain C: R.201 Chain D: D.97 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.97, C:R.201 EDO.12: 4 residues within 4Å: Chain C: G.251, K.252, E.253, Q.254 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.253, C:Q.254 EDO.13: 5 residues within 4Å: Chain C: R.233, W.243 Chain D: Q.9, V.10, M.100 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.233, C:W.243, D:V.10, D:V.10, D:M.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komine-Aizawa, S. et al., MHC-restricted Ag85B-specific CD8+T cells are enhanced by recombinant BCG prime and DNA boost immunization in mice. Eur.J.Immunol. (2019)

Release Date

2018-05-09

Peptides

H-2 class I histocompatibility antigen, K-D alpha chain: AC
Beta-2-microglobulin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

H-2 class I histocompatibility antigen, K-D alpha chain

Beta-2-microglobulin

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