SMTL ID : 8d5f.1

The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-mer

Ligands

1 x THR- GLY- ALA- ALA- ARG- PHE- ASP- GLU- PHE: Transcription initiation factor IIB(Non-covalent)

THR-GLY-ALA-ALA-ARG-PHE-ASP-GLU-PHE.1: 26 residues within 4Å: Chain A: Y.6, Y.58, E.62, R.65, N.69, S.72, F.73, V.75, D.76, T.79, Y.83, L.94, W.96, W.113, F.115, Y.122, T.142, K.145, W.146, A.149, A.151, R.154, Y.158, E.162, W.166, Y.170 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:Y.58, A:F.73, A:D.76, A:L.94, A:W.96, A:W.96, A:W.113, A:F.115, A:Y.122, A:Y.122, A:W.146, A:W.146, A:Y.158, A:W.166 Hydrogen bonds: A:Y.6, A:E.62, A:R.65, A:N.69, A:N.69, A:D.76, A:Y.83, A:E.162, A:Y.170 Water bridges: A:E.62, A:S.72, A:S.72, A:S.72, A:D.76, A:D.76, A:T.79, A:R.154, A:D.155 Salt bridges: A:D.76, A:K.145, A:K.145, A:R.154 pi-Cation interactions: A:F.73, A:W.96

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: H.187 Chain B: Y.11, S.12, P.15, P.16, W.96, R.98, M.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.12, B:W.96, B:R.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Custodio, J.M. et al., Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2022-07-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

H-2 class I histocompatibility antigen, D-D alpha chain

Beta-2-microglobulin

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