SMTL ID : 6uln.1

Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GLY- ALA- ASP- GLY- VAL- GLY- LYS- SER- ALA: GLY-ALA-ASP-GLY-VAL-GLY-LYS-SER-ALA(Non-covalent)

GLY-ALA-ASP-GLY-VAL-GLY-LYS-SER-ALA.1: 27 residues within 4Å: Chain A: M.5, Y.7, Y.9, E.63, K.66, R.69, Q.70, T.73, V.76, S.77, N.80, Y.84, R.97, Y.99, T.143, K.146, W.147, A.150, E.152, R.156, Y.159, W.167, Y.171 Chain C: Q.98, A.99 Chain D: Y.50, E.51 39 PLIP interactions: 33 interactions with chain A, 1 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: A:R.69, A:Y.99, A:A.150, A:Y.159 Hydrogen bonds: A:Y.7, A:E.63, A:S.77, A:N.80, A:Y.84, A:R.97, A:Y.99, A:Y.99, A:K.146, A:E.152, A:R.156, A:Y.171, A:Y.171, D:Y.50, C:Q.98 Water bridges: A:Y.9, A:E.63, A:R.69, A:R.69, A:Q.70, A:Q.70, A:Q.70, A:N.80, A:R.97, A:K.146, A:E.152, A:E.152, A:R.156, A:R.156, C:Q.98, C:Q.98, C:Q.98, C:Q.98 Salt bridges: A:K.146, A:R.156

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

SO4.2: 5 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: Y.63 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.63, A:D.30 Salt bridges: B:K.58 Water bridges: A:R.6 SO4.9: 4 residues within 4Å: Chain C: R.168 Chain D: V.165, H.166, S.167 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.166, D:S.167, C:R.168

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: N.127, E.128, D.129, S.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.128, A:D.129 GOL.4: 7 residues within 4Å: Chain A: V.231, R.234, W.244 Chain B: Q.8, V.9, V.93, M.99 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.8, B:V.9, A:R.234 Water bridges: B:V.9 GOL.5: 3 residues within 4Å: Chain A: S.92, D.119 Chain B: I.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.92, B:I.1, B:I.1 Water bridges: A:T.94, A:D.119 GOL.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain D: R.15, L.82, L.83, G.84 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.15, D:R.15, D:G.84 GOL.11: 3 residues within 4Å: Chain A: R.151 Chain D: H.29, Y.100 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.100, A:R.151

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.7: 1 residues within 4Å: Chain D: D.184 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.184, H2O.15 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sim, M.J.W. et al., High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-05-27

Peptides

HLA class I antigen: A
Beta-2-microglobulin: B
TCR-V-alpha-4*01: C
TCR-V-beta-5-6*01: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

HLA class I antigen

Beta-2-microglobulin

TCR-V-alpha-4*01

TCR-V-beta-5-6*01

Related Entries With Identical Sequence