SMTL ID : 6o9c.1

Crystal structure of HLA-A3*01 in complex with a mutant beta-catenin peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-mer

Ligands

1 x THR- THR- ALA- PRO- PHE- LEU- SER- GLY- LYS: Catenin beta-1(Non-covalent)

THR-THR-ALA-PRO-PHE-LEU-SER-GLY-LYS.1: 23 residues within 4Å: Chain A: M.8, Y.10, M.48, Y.62, E.66, N.69, T.76, D.80, T.83, Y.87, I.98, Y.102, R.117, D.119, W.136, T.146, K.149, W.150, E.155, Q.158, Y.162, W.170, Y.174 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.10, A:Y.62, A:D.80, A:Y.102, A:W.136, A:T.146, A:W.150, A:Y.162, A:W.170 Hydrogen bonds: A:E.66, A:N.69, A:D.80, A:D.80, A:Y.102, A:D.119, A:T.146, A:E.155, A:Q.158, A:Y.174, A:Y.174 Salt bridges: A:K.149

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 4 residues within 4Å: Chain A: N.130, D.132, R.134, S.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.135 Salt bridges: A:D.132, A:R.134 MES.10: 6 residues within 4Å: Chain A: A.214, F.244 Chain B: Y.46, S.77, K.78, Y.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.78

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

SO4.3: 3 residues within 4Å: Chain A: R.38, A.43, A.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.44 Salt bridges: A:R.38 SO4.4: 3 residues within 4Å: Chain A: E.235, T.236, K.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.236, A:T.236 Water bridges: A:K.246, A:K.246 Salt bridges: A:K.246 SO4.5: 2 residues within 4Å: Chain A: R.24 Chain B: H.71 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.24, B:H.71 SO4.6: 3 residues within 4Å: Chain A: D.223, G.224, R.276 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.276 SO4.7: 3 residues within 4Å: Chain A: D.140, M.141, A.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.141, A:A.142 SO4.8: 2 residues within 4Å: Chain A: W.170, R.173 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.173 SO4.9: 2 residues within 4Å: Chain A: Q.90 Chain B: A.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.90 SO4.11: 2 residues within 4Å: Chain B: R.23, T.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.24 SO4.12: 4 residues within 4Å: Chain B: K.61, F.90, T.91, Y.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.91, B:T.91, B:T.91, B:Y.98 Salt bridges: B:K.61 SO4.13: 3 residues within 4Å: Chain A: D.241 Chain B: R.32, H.33 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.32, B:H.33

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 1 residues within 4Å: Chain B: S.40 No protein-ligand interaction detected (PLIP) PEG.15: 3 residues within 4Å: Chain B: K.26, I.27, K.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.27, B:K.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, M.S. et al., An engineered antibody fragment targeting mutant beta-catenin via major histocompatibility complex I neoantigen presentation. J.Biol.Chem. (2019)

Release Date

2019-11-13

Peptides

HLA class I histocompatibility antigen, A-3 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-3 alpha chain

Beta-2-microglobulin

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