SMTL ID : 8stm.1

Crystal structure of KRAS-G75A mutant, GDP-bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 residues within 4Å: Chain A: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:V.30, A:Y.33, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:D.58 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118 GDP.3: 20 residues within 4Å: Chain B: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.4 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:D.31, B:D.31, B:Y.33, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:S.18, B:S.18, B:S.18, B:Y.33, B:D.58 Salt bridges: B:K.17, B:D.120 pi-Stacking: B:F.29, B:F.29 pi-Cation interactions: B:K.118 GDP.5: 19 residues within 4Å: Chain C: A.12, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.6 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:G.14, C:V.15, C:G.16, C:K.17, C:S.18, C:A.19, C:V.30, C:Y.33, C:N.117, C:K.118, C:K.118, C:A.147, C:K.148 Water bridges: C:K.17, C:K.17, C:S.18, C:S.18, C:S.18, C:Y.33, C:Y.33, C:D.58 Salt bridges: C:K.17, C:D.120 pi-Stacking: C:F.29, C:F.29 pi-Cation interactions: C:K.118 GDP.7: 19 residues within 4Å: Chain D: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.8 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:G.14, D:V.15, D:G.16, D:K.17, D:S.18, D:A.19, D:D.31, D:Y.33, D:N.117, D:K.118, D:K.118, D:S.146, D:A.147, D:K.148 Water bridges: D:S.18, D:Y.33 Salt bridges: D:K.17, D:D.120 pi-Stacking: D:F.29, D:F.29 pi-Cation interactions: D:K.118

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.18, P.35 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain B: S.18 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.18, H2O.3, H2O.3, H2O.3, H2O.3 MG.6: 2 residues within 4Å: Chain C: S.18 Ligands: GDP.5 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:S.18, H2O.5, H2O.5, H2O.5, H2O.5 MG.8: 2 residues within 4Å: Chain D: S.18 Ligands: GDP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.18, H2O.7, H2O.7, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, M.H. et al., Allosteric Regulation of Switch-II Domain Controls KRAS Oncogenicity. Cancer Res. (2023)

Release Date

2023-08-23

Peptides

GTPase KRas: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GTPase KRas