SMTL ID : 6q3k.1

Engineered Human HLA_A2 MHC Class I molecule in complex with NV9 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASN- LEU- VAL- PRO- MET- VAL- ALA- THR- VAL: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL(Non-covalent)

ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL.1: 24 residues within 4Å: Chain A: M.6, Y.8, F.10, M.46, E.64, K.67, V.68, H.71, T.74, V.77, D.78, R.98, Y.100, Y.117, Y.124, T.144, K.147, W.148, V.153, Y.160, T.164, W.168, Y.172 Ligands: GOL.10 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:Y.8, A:F.10, A:K.67, A:V.68, A:V.77, A:Y.100, A:Y.117, A:Y.124, A:T.144, A:W.148, A:V.153, A:Y.160, A:Y.160, A:W.168 Hydrogen bonds: A:Y.8, A:E.64, A:D.78, A:Y.100, A:T.144, A:K.147, A:W.168, A:Y.172 Water bridges: A:K.67, A:K.67, A:H.71, A:D.78, A:R.98, A:K.147, A:W.148 Salt bridges: A:K.147

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.7, F.9, Y.28, D.30, D.31 Chain B: Y.64 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.7, A:D.31, A:D.31 Water bridges: B:Y.64 GOL.10: 9 residues within 4Å: Chain A: R.98, H.115, W.148, V.153, L.157 Ligands: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL.1, ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL.1, ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL.1, ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.98, A:R.98 Water bridges: A:L.157

7 x CO: COBALT (II) ION(Non-covalent)(Non-functional Binders)

CO.3: 2 residues within 4Å: Chain A: H.198, E.199 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.198, H2O.2, H2O.3 CO.4: 1 residues within 4Å: Chain A: H.152 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.152, H2O.7, H2O.9 CO.5: 2 residues within 4Å: Chain A: Q.219, H.261 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.261, H2O.5, H2O.6, H2O.8 CO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CO.7: 1 residues within 4Å: Chain A: E.155 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.155, A:E.155, H2O.12, H2O.13, H2O.13 CO.8: 1 residues within 4Å: Chain A: H.192 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:H.192, H2O.11 CO.9: 1 residues within 4Å: Chain B: H.52 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.52, H2O.17, H2O.18, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meijers, R. et al., Engineered Human HLA_A2MHC Class I molecule in complex with NV9 peptide. Sci Immunol (2019)

Release Date

2019-07-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

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