SMTL ID : 9eb6.1

Chicken YF1.7*1 presenting myristoylated peptide derived from tegument protein CIRC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- ILE- ILE- PHE- SER: Peptide derived from tegument protein CIRC(Non-covalent)

GLY-ILE-ILE-PHE-SER.1: 12 residues within 4Å: Chain A: D.71, W.74, N.75, R.78, L.79, P.80, M.92, Y.112, F.119, T.139, W.143 Ligands: MYR.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.78, A:L.79, A:Y.112, A:F.119, A:F.119, A:T.139, A:W.143 Hydrogen bonds: A:N.75, A:N.75, A:N.75 Water bridges: A:T.139, A:R.142, A:W.153

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 7 residues within 4Å: Chain A: Q.264, P.265, G.266, L.267, F.268 Ligands: CL.6, NA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.267

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: V.184, R.185, V.186, W.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.186 Water bridges: A:V.184, A:V.184, A:R.185, A:S.269

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: S.269 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: P.20, R.21, S.38 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Ligands: PGE.2, NA.8 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 2 residues within 4Å: Chain A: P.80, E.81 No protein-ligand interaction detected (PLIP) NA.8: 4 residues within 4Å: Chain A: G.266, F.268 Ligands: PGE.2, CL.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.265

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.9: 15 residues within 4Å: Chain A: Y.7, L.9, I.24, G.34, T.35, A.43, Q.61, K.64, A.65, G.68, D.71, M.94, Y.112, W.153 Ligands: GLY-ILE-ILE-PHE-SER.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.7, A:L.9, A:I.24, A:A.43, A:Q.61, A:A.65, A:W.153, A:W.153 Hydrogen bonds: A:Y.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khandokar, Y. et al., Molecular basis for presentation of N-myristoylated peptides by the chicken YF1∗7.1 molecule. J.Biol.Chem. (2025)

Release Date

2025-07-23

Peptides

MHC Rfp-Y class I alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MHC Rfp-Y class I alpha chain

Beta-2-microglobulin

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