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

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylcholine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: E.59, E.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.59, A:E.59, A:E.62, A:E.62 ZN.2: 3 residues within 4Å: Chain A: A.1, H.4, Q.181 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:H.4 ZN.3: 1 residues within 4Å: Chain A: H.198 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.198, H2O.2 ZN.4: 1 residues within 4Å: Chain A: E.139 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.139, A:E.139 ZN.5: 2 residues within 4Å: Chain A: H.193 Chain B: D.99 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.193

19 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: F.9, Y.28, D.30, D.31 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: L.231, V.232, E.233, K.244 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: N.128, E.129, D.130, S.133 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: R.109, L.110, E.162, L.166 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: A.1, H.4, L.180, Q.181, R.182, Y.210, P.211, E.265 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: G.2, L.104, G.105, P.106 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: S.3, H.4, S.5, D.30, D.103 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: R.49 Ligands: EDO.25 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: P.16, G.17, R.18, G.19 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: P.51, W.52, Q.55 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: T.179, R.182, Y.210, G.240 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: M.6, Y.8, Q.64, Y.160, S.168, Y.172 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: Y.115, W.148, V.153, W.157 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: R.7, M.99, Y.114, Q.116 Chain B: K.59 Ligands: EDO.24 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain A: D.107 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain A: W.205, L.207, R.235, Q.243 Chain B: Y.11, S.12, R.13, H.14, P.15 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: S.58, K.59, D.60 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain A: F.9, M.99, Q.116 Chain B: F.57, S.58, K.59, W.61 Ligands: EDO.19 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: G.238 Chain B: S.53, L.66, Y.68 Ligands: EDO.13 Ligand excluded by PLIP

1 x EKG: (2R)-2,3-dihydroxypropyl hexadecanoate(Non-covalent)

EKG.21: 14 residues within 4Å: Chain A: Y.8, S.10, F.23, R.67, V.68, A.71, F.75, T.98, M.99, S.100, Y.115, Q.156, W.157, Y.160 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.8, A:F.23, A:V.68, A:A.71, A:F.75, A:F.75, A:Y.160 Hydrogen bonds: A:Q.156 Salt bridges: A:R.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shima, Y. et al., Crystal structures of lysophospholipid-bound MHC class I molecules. J.Biol.Chem. (2020)

Release Date

2020-04-22

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

MHC class I antigen

Beta-2-microglobulin

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