SMTL ID : 7na5.1

Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoantigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x TYR- GLY- PHE- ARG- ASN- VAL- VAL- HIS- ILE: Heat shock factor protein 2(Non-covalent)

TYR-GLY-PHE-ARG-ASN-VAL-VAL-HIS-ILE.1: 36 residues within 4Å: Chain A: M.6, Y.8, Y.60, R.63, E.64, K.67, G.70, Q.71, W.74, V.77, S.78, N.81, L.82, Y.85, Q.98, F.117, Y.124, T.144, K.147, W.148, S.151, H.156, Y.157, Y.160, E.164, W.168, Y.172 Chain C: Q.32, Y.33, Y.95, N.96 Chain D: E.97, P.98, Y.101 Ligands: GOL.6, GOL.11 42 PLIP interactions: 31 interactions with chain A, 3 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: A:W.74, A:W.74, A:V.77, A:L.82, A:Y.85, A:Y.157, A:Y.160, A:Y.160, A:E.164, A:E.164, A:W.168, A:W.168, D:Y.101, C:Y.33, C:Y.95 Hydrogen bonds: A:Y.8, A:Y.8, A:Y.60, A:E.64, A:Q.71, A:Q.71, A:S.78, A:N.81, A:Q.98, A:Q.98, A:Y.172, D:Y.101, C:Y.95 Water bridges: A:S.100, A:S.100, A:S.100, A:Y.160, D:D.57, C:N.96, C:N.96, C:N.96, C:N.96, C:N.96 Salt bridges: A:K.147 pi-Stacking: A:Y.157, A:W.168 pi-Cation interactions: A:K.67

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: F.9, Y.28, N.31 Chain B: F.57, K.59, Y.64 Ligands: SO4.8, GOL.10 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.31, B:K.59, B:Y.64, B:Y.64 Water bridges: A:S.5, A:R.7, B:K.59 GOL.3: 6 residues within 4Å: Chain A: E.33, R.36, R.49 Chain B: S.53, D.54, S.56 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.54, A:E.33, A:R.36, A:R.49 GOL.4: 4 residues within 4Å: Chain A: R.49, A.50, P.51, E.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.50 GOL.5: 4 residues within 4Å: Chain A: Q.116, D.123 Chain B: K.59, D.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.123 GOL.6: 5 residues within 4Å: Chain A: Q.66, Q.73 Chain D: M.56, D.57 Ligands: TYR-GLY-PHE-ARG-ASN-VAL-VAL-HIS-ILE.1 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: A:Q.66, D:M.56 Water bridges: D:D.57, D:D.57, D:D.57, C:N.96 GOL.7: 3 residues within 4Å: Chain A: T.183, D.184, S.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.185, A:S.185 GOL.9: 5 residues within 4Å: Chain B: E.75, D.77, W.96, D.97, R.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.77, B:R.98, B:R.98 GOL.10: 4 residues within 4Å: Chain A: N.31 Chain B: K.59 Ligands: GOL.2, SO4.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.31, B:K.59, B:K.59 Water bridges: A:A.212 GOL.11: 9 residues within 4Å: Chain A: W.74, L.115, W.148, A.153, H.156 Ligands: TYR-GLY-PHE-ARG-ASN-VAL-VAL-HIS-ILE.1, TYR-GLY-PHE-ARG-ASN-VAL-VAL-HIS-ILE.1, TYR-GLY-PHE-ARG-ASN-VAL-VAL-HIS-ILE.1, TYR-GLY-PHE-ARG-ASN-VAL-VAL-HIS-ILE.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.156 GOL.12: 4 residues within 4Å: Chain A: Q.150 Chain C: S.50, F.52 Chain D: Y.101 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.50 GOL.14: 11 residues within 4Å: Chain D: Q.26, H.30, N.31, A.32, M.33, Y.50, Y.52, Q.53, S.69, K.72, H.74 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.26, D:H.30, D:Q.53, D:K.72 GOL.15: 6 residues within 4Å: Chain D: D.154, H.155, V.156, P.175, Q.176, A.177 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.154, D:V.156, D:V.156, D:A.177 GOL.16: 5 residues within 4Å: Chain D: P.9, K.10, Y.11, H.212, T.229 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.10, D:Y.11, D:H.212, D:T.229, D:T.229

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

SO4.8: 6 residues within 4Å: Chain A: S.5, R.7, N.31 Chain B: K.59 Ligands: GOL.2, GOL.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.5, A:S.5, A:N.31 Water bridges: A:N.31 Salt bridges: A:R.7, B:K.59 SO4.13: 4 residues within 4Å: Chain C: H.65, N.67, S.70, H.72 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.67, C:S.70 Salt bridges: C:H.65, C:H.72 SO4.17: 3 residues within 4Å: Chain D: S.62, R.64, K.83 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.62 Salt bridges: D:R.64, D:K.83 SO4.18: 3 residues within 4Å: Chain D: V.167, H.168, S.169 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.168, D:S.169 Salt bridges: D:H.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Structure of the TCR-H2DB ternary complex with melanoma HSF2 neoantigen YGFRNVVHI. To be Published

Release Date

2022-06-22

Peptides

H-2 class I histocompatibility antigen, D-B alpha chain: A
Beta-2-microglobulin: B
47BE7 TCR alpha chain: C
47BE7 TCR beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

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

Beta-2-microglobulin

47BE7 TCR alpha chain

47BE7 TCR beta chain

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