SMTL ID : 6gb7.4 (3 other biounits)

Structure of H-2Db with scoop loop from tapasin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 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: 17 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.45, E.63, K.66, Q.70, W.73, Q.97, S.150, A.152, H.155, Y.156, Y.159, E.163, W.167, Y.171 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.7, A:A.152, A:H.155, A:Y.156, A:Y.159, A:Y.159, A:W.167, A:W.167 Hydrogen bonds: A:Y.7, 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-Stacking: A:W.167 pi-Cation interactions: A:K.66

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

SO4.2: 5 residues within 4Å: Chain A: R.14, P.15, A.89, G.90, G.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.90, A:G.91, A:G.91

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, N.30 Chain B: F.57, Y.64 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.30, B:Y.64, B:Y.64 Water bridges: A:N.30 GOL.4: 4 residues within 4Å: Chain A: P.235, F.241 Chain B: Y.64, L.66 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:E.32, B:S.56

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
G

B
H

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

Beta-2-microglobulin

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