SMTL ID : 4pg9.1

MHC Class I in complex with Sendai virus nucleoprotein peptide FAPGNYPAL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PHE- ALA- PRO- GLY- ASN- TYR- PRO- ALA- LEU: Sendai virus nucleoprotein(Non-covalent)

PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.1: 27 residues within 4Å: Chain A: Y.33, V.35, Y.71, Y.85, R.88, E.89, K.92, N.96, S.99, F.100, D.103, T.106, L.107, Y.110, S.125, Q.140, Y.142, Y.149, T.169, K.172, W.173, E.178, Y.185, T.189, W.193, Y.197 Ligands: GOL.11 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:Y.33, A:F.100, A:F.100, A:D.103, A:L.107, A:Y.149, A:T.169, A:W.173, A:E.178, A:Y.185, A:T.189, A:W.193, A:W.193 Hydrogen bonds: A:Y.33, A:Y.33, A:Y.85, A:E.89, A:K.92, A:N.96, A:N.96, A:S.99, A:D.103, A:Y.197 Water bridges: A:D.103, A:T.106, A:S.125 Salt bridges: A:K.172 pi-Cation interactions: A:K.92

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.192, W.193, R.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.192 GOL.3: 6 residues within 4Å: Chain A: R.47 Chain B: I.36, E.37, I.38, M.52 Ligands: GOL.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.38, B:I.38, A:R.47, A:R.47 GOL.4: 3 residues within 4Å: Chain A: H.217, H.218, S.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.217, A:H.218 GOL.5: 2 residues within 4Å: Chain A: A.161, A.162 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.164 GOL.6: 10 residues within 4Å: Chain A: D.56, T.57, P.261, A.262, G.263, D.264, G.265, T.266, F.267 Chain B: D.54 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.56, A:A.262, A:G.263, A:D.264, A:G.265, A:T.266 Water bridges: A:E.58 GOL.7: 6 residues within 4Å: Chain A: V.38, R.47, M.49 Chain B: P.34, I.36 Ligands: GOL.3 No protein-ligand interaction detected (PLIP) GOL.8: 9 residues within 4Å: Chain A: W.230 Chain B: V.10, Y.11, S.12, H.14, P.15, P.16, W.96, D.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.10, B:S.12, B:S.12 GOL.9: 5 residues within 4Å: Chain A: E.258 Chain B: Y.27, S.56, F.57, Y.64 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.27, B:S.56, B:F.57, A:E.258 GOL.10: 6 residues within 4Å: Chain A: K.212, L.232, G.233 Chain B: R.13, H.14, P.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.13, B:R.13 GOL.11: 6 residues within 4Å: Chain A: R.181, L.182, Y.185 Ligands: PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.1, PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.1, PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garstka, M.A. et al., The first step of peptide selection in antigen presentation by MHC class I molecules. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-01-07

Peptides

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

Beta-2-microglobulin

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