SMTL ID : 5ib4.1

Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR and Nickel

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- ARG- LYS- TRP- ARG- ARG- TRP- HIS- LEU: Vasoactive intestinal polypeptide receptor 1(Non-covalent)

ARG-ARG-LYS-TRP-ARG-ARG-TRP-HIS-LEU.1: 33 residues within 4Å: Chain A: Y.7, H.9, T.24, E.45, Y.59, R.62, E.63, Q.65, I.66, C.67, A.69, K.70, T.73, E.76, D.77, T.80, L.81, Y.84, L.95, Y.99, H.114, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, E.163, W.167, Y.171 Ligands: NI.5 40 PLIP interactions: 40 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:R.62, A:I.66, A:I.66, A:D.77, A:L.81, A:L.95, A:Y.123, A:T.143, A:W.147, A:V.152, A:V.152, A:Q.155, A:L.156, A:L.156, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:T.24, A:T.24, A:T.24, A:R.62, A:R.62, A:E.63, A:D.77, A:D.77, A:Y.99, A:Y.99, A:T.143, A:Q.155, A:Q.155, A:Y.159, A:Y.171 Water bridges: A:T.80, A:W.147 Salt bridges: A:E.45, A:E.63, A:K.146, A:E.163

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

NI.2: 3 residues within 4Å: Chain A: G.1, S.2, H.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.1, A:H.3, H2O.2, H2O.5, H2O.5 NI.5: 2 residues within 4Å: Chain A: E.76 Ligands: ARG-ARG-LYS-TRP-ARG-ARG-TRP-HIS-LEU.1 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.64, A:D.30 GOL.4: 1 residues within 4Å: Chain B: H.52 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.51, B:E.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Driller, R. et al., Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype. J.Biol.Chem. (2019)

Release Date

2017-02-01

Peptides

HLA class I histocompatibility antigen, B-27 alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I histocompatibility antigen, B-27 alpha chain

Beta-2-microglobulin

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