SMTL ID : 3vj6.1

Structure of the MHC class Ib molecule Qa-1b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ALA- MET- ALA- PRO- ARG- THR- LEU- LEU- LEU: Qdm peptide(Non-covalent)

ALA-MET-ALA-PRO-ARG-THR-LEU-LEU-LEU.1: 27 residues within 4Å: Chain A: Y.7, I.24, M.45, E.63, K.66, A.67, M.70, N.73, F.74, N.77, T.80, L.81, Y.84, L.95, W.97, Y.99, E.116, I.124, W.133, S.143, K.146, E.152, Q.155, Q.156, Y.159, W.167, Y.171 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:N.73, A:L.81, A:L.95, A:Y.99, A:I.124, A:W.133, A:W.133, A:E.152, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:N.77, A:N.77, A:Y.99, A:Y.99, A:V.150, A:Q.155, A:Q.156, A:Y.171, A:Y.171 Water bridges: A:N.73, A:N.77, A:T.80, A:E.152, A:E.152, A:E.152 Salt bridges: A:K.146, A:E.152

4 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 1 residues within 4Å: Chain A: H.260 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.260, H2O.4, H2O.5, H2O.7 NI.3: 1 residues within 4Å: Chain A: H.192 No protein-ligand interaction detected (PLIP) NI.4: 1 residues within 4Å: Chain B: H.35 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.35, H2O.9, H2O.10, H2O.10 NI.5: 1 residues within 4Å: Chain B: H.68 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.68, H2O.9, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, L. et al., A structural basis for antigen presentation by the MHC class Ib molecule, Qa-1b. J.Immunol. (2012)

Release Date

2012-03-14

Peptides

H-2 class I histocompatibility antigen, D-37 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, D-37 alpha chain

Beta-2-microglobulin

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