SMTL ID : 4pge.1

MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNYPAW

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-TRP.1: 29 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, L.107, Y.110, I.121, V.123, S.125, Q.140, Y.142, A.143, Y.149, T.169, K.172, W.173, E.178, Y.185, T.189, W.193, Y.197 Ligands: GOL.9 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:Y.33, A:N.96, A:F.100, A:F.100, A:L.107, A:I.121, A:V.123, A:Y.142, A:Y.149, A:Y.149, 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:S.99, A:D.103, A:S.125, A:S.125, A:E.178, A:Y.197 Water bridges: A:N.96, A:S.99, A:D.103, A:T.106 Salt bridges: A:K.172 pi-Cation interactions: A:K.92

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: M.49, V.51, E.58, R.61 Chain B: M.52, S.53, D.54, M.55 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.55, A:E.58 GOL.4: 2 residues within 4Å: Chain A: T.208, Q.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.208 GOL.5: 2 residues within 4Å: Chain A: H.218, S.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.217, A:S.219 GOL.7: 6 residues within 4Å: Chain A: K.212, L.232, G.233 Chain B: R.13, H.14, P.15 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.212, A:L.232, B:R.13, B:R.13 GOL.8: 7 residues within 4Å: Chain A: W.230 Chain B: V.10, Y.11, S.12, W.96, D.97, M.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.12, B:S.12, B:D.97 GOL.9: 6 residues within 4Å: Chain A: R.181, L.182, Y.185 Ligands: PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-TRP.1, PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-TRP.1, PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-TRP.1 No protein-ligand interaction detected (PLIP)

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: A.161, A.162, D.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.162 MPD.6: 6 residues within 4Å: Chain A: R.47, M.49 Chain B: P.34, I.36, M.55, I.65 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.65, A:R.47 Hydrogen bonds: B:P.34 Water bridges: B:H.35, B:I.36, A:R.47

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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