SMTL ID : 6o9b.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

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

THR-THR-ALA-PRO-SER-LEU-SER-GLY-LYS.1: 22 residues within 4Å: Chain A: M.8, Y.10, Y.62, E.66, N.69, A.72, T.76, D.80, T.83, Y.87, I.98, Y.102, R.117, D.119, T.146, K.149, W.150, E.155, Q.158, Y.162, W.170, Y.174 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:Y.10, A:Y.62, A:D.80, A:Y.102, A:T.146, A:W.150, A:W.150, A:Y.162, A:W.170 Hydrogen bonds: A:E.66, A:N.69, A:A.72, A:D.80, A:Y.102, A:D.119, A:T.146, A:E.155, A:Y.174, A:Y.174 Water bridges: A:N.69, A:Q.73, A:Q.73, A:D.80, A:Y.102, A:Y.102, A:R.117, A:R.117, A:K.149 Salt bridges: A:K.149

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: R.17, R.24 Chain B: S.53, D.54, H.71, Y.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.17, A:R.24, A:R.24 PG4.12: 10 residues within 4Å: Chain A: R.9, F.11, M.101, R.114, Y.116, Q.118 Chain B: S.77, K.78, W.80 Ligands: MES.13 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.114, B:K.78, B:K.78

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

MES.3: 4 residues within 4Å: Chain A: N.130, D.132, R.134, S.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.135 Water bridges: A:R.134 Salt bridges: A:D.132, A:R.134 MES.13: 10 residues within 4Å: Chain A: A.214, T.236, F.244 Chain B: Y.46, S.77, K.78, Y.83 Ligands: PEG.6, PG4.12, MES.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.78 MES.14: 7 residues within 4Å: Chain A: E.235, T.236, K.246 Chain B: S.77, K.78, D.79 Ligands: MES.13 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.236, A:T.236, B:K.78, B:D.79 Water bridges: A:K.246, A:K.246 Salt bridges: A:E.235, A:K.246, B:D.79

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 7 residues within 4Å: Chain A: S.5, H.6, D.32, L.182, R.184, T.185, E.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.267 pi-Cation interactions: A:H.6 IMD.5: 3 residues within 4Å: Chain A: E.169, R.172, R.173 No protein-ligand interaction detected (PLIP)

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

PEG.6: 7 residues within 4Å: Chain A: R.9, Y.30, D.32, D.33, F.244 Chain B: Y.83 Ligands: MES.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.9 PEG.7: 4 residues within 4Å: Chain A: R.47, M.48, E.56, W.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.48, A:E.56 PEG.15: 9 residues within 4Å: Chain A: H.191, T.193, W.207, Q.245 Chain B: S.31, R.32, H.33, P.34, R.117 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.191, A:Q.245, B:S.31 PEG.16: 6 residues within 4Å: Chain B: D.54, I.55, E.56, N.103, H.104, V.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.56, B:N.103

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

EDO.8: 5 residues within 4Å: Chain A: S.5, H.6, S.7, D.32, D.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.105 EDO.9: 5 residues within 4Å: Chain A: H.195, I.197, T.203, R.205 Chain B: D.116 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.116, A:T.203 EDO.10: 1 residues within 4Å: Chain A: G.19 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: Y.87, M.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.141 EDO.17: 5 residues within 4Å: Chain B: E.56, V.57, D.58, R.101, N.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.58, B:D.58, B:N.103 EDO.18: 2 residues within 4Å: Chain B: I.27, K.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.111 EDO.19: 3 residues within 4Å: Chain B: T.106, L.107, S.108 No protein-ligand interaction detected (PLIP)

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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