SMTL ID : 9eb3.1

Chicken YF1.7*1 presenting N-myristoylated glycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BJU: N-tetradecanoylglycine(Non-covalent)

BJU.1: 16 residues within 4Å: Chain A: Y.7, L.9, G.26, G.34, T.35, A.43, Q.61, K.64, A.65, G.68, D.71, M.94, F.96, Y.112, Y.149, W.153 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.7, A:L.9, A:A.43, A:K.64, A:F.96, A:F.96, A:W.153 Hydrogen bonds: A:D.71, A:Y.112 Water bridges: A:D.71

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: G.266, L.267, F.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.267, A:L.267 GOL.3: 3 residues within 4Å: Chain A: G.1, H.3, E.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.3 GOL.4: 4 residues within 4Å: Chain A: I.106, G.158, V.162, R.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.166, A:R.166 GOL.9: 8 residues within 4Å: Chain A: F.8, Y.27, D.30, R.207 Chain B: S.54, F.55, D.57, Q.62 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.30, A:D.30, B:S.54, B:F.55

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: W.74, R.78, R.82, T.139, R.142, W.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.74 Salt bridges: A:R.78, A:R.82, A:R.142 SO4.6: 1 residues within 4Å: Chain A: R.185 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.185 SO4.7: 5 residues within 4Å: Chain A: M.19, P.20, R.21, S.38, K.39 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.19, A:R.21, A:S.38 Water bridges: A:E.69, A:E.69

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

CL.8: 1 residues within 4Å: Chain A: W.270 Ligand excluded by PLIP

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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