SMTL ID : 6gb5.2 (1 other biounit)

Structure of H-2Db with truncated SEV peptide and GL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PHE- ALA- PRO- GLY- ASN- TYR- PRO: PHE-ALA-PRO-GLY-ASN-TYR-PRO(Non-covalent)

PHE-ALA-PRO-GLY-ASN-TYR-PRO.1: 23 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.45, Y.59, R.62, E.63, K.66, Q.70, W.73, F.74, Q.97, S.99, S.150, G.151, A.152, H.155, Y.156, Y.159, E.163, W.167, Y.171 Ligands: GLY-LEU.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.7, A:W.73, A:A.152, A:H.155, A:Y.159, A:E.163, A:E.163, A:W.167, A:W.167 Hydrogen bonds: A:Y.7, A:Y.59, A:E.63, A:Q.70, A:Q.70, A:Q.97, A:Q.97, A:Y.156, A:Y.159, A:Y.171 pi-Cation interactions: A:K.66

1 x GLY- LEU: GLY-LEU(Non-covalent)

GLY-LEU.2: 10 residues within 4Å: Chain A: W.73, S.77, N.80, L.81, Y.84, L.95, T.143, K.146, W.147 Ligands: PHE-ALA-PRO-GLY-ASN-TYR-PRO.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.73, A:L.81, A:L.95, A:W.147 Hydrogen bonds: A:S.77, A:N.80, A:T.143 Salt bridges: A:K.146

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

SO4.3: 3 residues within 4Å: Chain A: P.15, A.89, G.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.90 SO4.4: 1 residues within 4Å: Chain A: R.145 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.145 SO4.5: 1 residues within 4Å: Chain A: R.111 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.111 SO4.6: 3 residues within 4Å: Chain A: E.166, W.167, R.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.167

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: R.6, F.8, Y.27, N.30 Chain B: F.56, K.58, Y.63 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.58, B:Y.63, B:Y.63, A:N.30, A:N.30 Water bridges: A:N.30 GOL.8: 7 residues within 4Å: Chain A: R.234 Chain B: I.7, Q.8, V.9, Y.94, D.96, M.99 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.7, B:V.9, B:Y.94, B:D.96, B:M.99, A:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hafstrand, I. et al., Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-03-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

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

Beta-2-microglobulin

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