SMTL ID : 5j6h.1

Recognition of the MHC class Ib molecule H2-Q10 by the natural killer cell receptor Ly49C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VAL- GLY- ILE- THR- ASN- VAL- ASP- LEU: VAL-GLY-ILE-THR-ASN-VAL-ASP-LEU(Non-covalent)

VAL-GLY-ILE-THR-ASN-VAL-ASP-LEU.1: 25 residues within 4Å: Chain A: M.6, Y.8, Y.60, R.63, E.64, R.67, N.71, S.74, F.75, V.77, S.78, Y.85, W.98, Y.100, Y.117, Y.124, T.144, K.147, W.148, Y.156, Y.157, Y.160, E.164, W.168, Y.172 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.60, A:F.75, A:W.98, A:W.98, A:Y.100, A:Y.117, A:Y.124, A:W.148, A:Y.156, A:Y.160, A:Y.160, A:Y.160, A:W.168, A:W.168 Hydrogen bonds: A:Y.8, A:E.64, A:R.67, A:N.71, A:N.71, A:S.74, A:S.74, A:S.78, A:Y.85, A:Y.100, A:Y.100, A:K.147, A:Y.156, A:Y.156, A:Y.157, A:Y.157, A:Y.172

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

NA.2: 6 residues within 4Å: Chain A: T.95, Q.97, A.118, Y.119, D.120, G.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.95, A:Q.97, A:G.121 NA.4: 7 residues within 4Å: Chain A: A.237, G.238 Chain B: R.13, I.23, N.25, L.66, H.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.13, B:R.13

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.3: 3 residues within 4Å: Chain A: P.48, R.49, E.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.49 pi-Cation interactions: A:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sullivan, L.C. et al., Recognition of the Major Histocompatibility Complex (MHC) Class Ib Molecule H2-Q10 by the Natural Killer Cell Receptor Ly49C. J.Biol.Chem. (2016)

Release Date

2016-07-13

Peptides

H-2 class I histocompatibility antigen, Q10 alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

H-2 class I histocompatibility antigen, Q10 alpha chain

Beta-2-microglobulin

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