SMTL ID : 9kfl.1

KRAS G12V and peptide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

homo-pentamer

Ligands

2 x GLU- ASP- VAL- VAL- GLY- GLY- CYS- CYS: TIG3 peptide(Non-covalent)

GLU-ASP-VAL-VAL-GLY-GLY-CYS-CYS.1: 6 residues within 4Å: Chain A: D.69, E.98, Q.99, R.102, V.103 Ligands: GLU-ASP-VAL-VAL-GLY-GLY-CYS-CYS.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.102 Salt bridges: A:R.102 GLU-ASP-VAL-VAL-GLY-GLY-CYS-CYS.2: 2 residues within 4Å: Chain A: R.73 Ligands: GLU-ASP-VAL-VAL-GLY-GLY-CYS-CYS.1 No protein-ligand interaction detected (PLIP)

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: S.17, Y.32, I.36, D.57, T.58, A.59 Ligands: GDP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.17, A:I.36 MG.5: 4 residues within 4Å: Chain B: S.17, D.33, P.34 Ligands: GDP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.17 MG.7: 4 residues within 4Å: Chain C: S.17, P.34, T.58 Ligands: GDP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.17 MG.9: 5 residues within 4Å: Chain D: S.17, P.34, T.58, A.59 Ligands: GDP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.17 MG.11: 5 residues within 4Å: Chain E: S.17, Y.32, D.33, P.34 Ligands: GDP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.17

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

GDP.4: 20 residues within 4Å: Chain A: A.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, Y.32, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:S.17, A:A.18, A:V.29, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28 GDP.6: 21 residues within 4Å: Chain B: A.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, D.30, Y.32, P.34, D.57, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:S.17, B:S.17, B:A.18, B:T.58, B:N.116, B:K.117, B:K.117, B:A.146, B:K.147 Salt bridges: B:K.16, B:D.119 pi-Stacking: B:F.28 GDP.8: 20 residues within 4Å: Chain C: A.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, Y.32, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.13, C:V.14, C:G.15, C:K.16, C:S.17, C:A.18, C:D.30, C:N.116, C:K.117, C:K.117, C:S.145, C:A.146, C:K.147 Salt bridges: C:K.16, C:D.119 pi-Stacking: C:F.28 GDP.10: 20 residues within 4Å: Chain D: V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, Y.32, P.34, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:S.17, D:S.17, D:V.29, D:Y.32, D:N.116, D:K.117, D:K.117, D:A.146, D:K.147 Salt bridges: D:K.16, D:D.119 pi-Stacking: D:F.28 GDP.12: 19 residues within 4Å: Chain E: A.11, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, Y.32, D.57, N.116, K.117, D.119, S.145, A.146, K.147 Ligands: MG.11 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.13, E:V.14, E:G.15, E:K.16, E:S.17, E:A.18, E:D.30, E:Y.32, E:D.57, E:N.116, E:K.117, E:S.145, E:A.146, E:K.147 Salt bridges: E:K.16, E:D.119 pi-Stacking: E:F.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ha, M.S. et al., KRAS G12V and TIG3 peptide complex. To Be Published

Release Date

2025-11-12

Peptides

Isoform 2B of GTPase KRas: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
H

E
K

Isoform 2B of GTPase KRas