SMTL ID : 8dvg.1

Structure of KRAS WT(7-16)-HLA-A*03:01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 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 SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: Y.30, P.238 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.73 SO4.4: 5 residues within 4Å: Chain A: R.117, W.150, E.155 Chain C: G.7, V.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.155, A:E.155, C:V.8 Salt bridges: A:R.117 SO4.5: 2 residues within 4Å: Chain A: Q.90 Chain B: A.20 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.19, B:A.20, A:Q.90 SO4.6: 1 residues within 4Å: Chain A: R.173 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.173 SO4.7: 4 residues within 4Å: Chain A: D.33, A.214, T.236 Chain B: Y.83 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.83 Hydrogen bonds: A:T.236 SO4.9: 4 residues within 4Å: Chain B: Q.22, R.23, T.24, K.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.24, B:T.24 Salt bridges: B:K.26 SO4.10: 2 residues within 4Å: Chain B: R.65, R.101 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.101 SO4.11: 4 residues within 4Å: Chain A: G.240 Chain B: L.85, Y.87 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.87 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: 4 residues within 4Å: Chain B: D.54, I.55, N.103, H.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.103 Water bridges: B:N.103, B:V.105 SO4.14: 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

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

PEG.8: 3 residues within 4Å: Chain A: R.24 Chain B: S.53, H.71 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.24, A:R.24, B:S.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wright, K.M. et al., Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen. Nat Commun (2023)

Release Date

2023-07-19

Peptides

HLA class I histocompatibility antigen, A-3 alpha chain: A
Beta-2-microglobulin: B
VAL-VAL-VAL-GLY-ALA-GLY-GLY-VAL-GLY-LYS: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class I histocompatibility antigen, A-3 alpha chain

Beta-2-microglobulin

VAL-VAL-VAL-GLY-ALA-GLY-GLY-VAL-GLY-LYS

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