SMTL ID : 7w5r.1

KRAS G12V and peptide complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.87 Å

Oligo State

homo-hexamer

Ligands

2 x LEU- TYR- ASP- VAL- ALA: LEU-TYR-ASP-VAL-ALA(Non-covalent)

LEU-TYR-ASP-VAL-ALA.1: 1 residues within 4Å: Chain B: Q.61 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.61 Hydrogen bonds: B:Q.61 LEU-TYR-ASP-VAL-ALA.2: 1 residues within 4Å: Chain F: G.60 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.16, S.17, P.34 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: K.16, S.17, D.57 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, I.36 Ligands: GDP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.17 MG.9: 4 residues within 4Å: Chain D: K.16, S.17, D.57 Ligands: GDP.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.17, D:D.57, D:D.57 MG.11: 4 residues within 4Å: Chain E: S.17, Y.32, P.34 Ligands: GDP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.17 MG.13: 5 residues within 4Å: Chain F: S.17, Y.32, D.33, P.34 Ligands: GDP.14 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.17

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

GDP.4: 17 residues within 4Å: Chain A: A.11, V.12, G.13, V.14, G.15, K.16, S.17, F.28, V.29, D.30, E.31, Y.32, P.34, K.117 Chain B: R.149, D.153 Ligands: MG.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.11, A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:Y.32, A:K.117, B:R.149 Salt bridges: A:K.16, A:E.31, B:D.153 GDP.6: 14 residues within 4Å: Chain B: A.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, E.31, Y.32, P.34, K.117 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.11, B:G.13, B:G.15, B:K.16, B:S.17, B:A.18, B:K.117 Salt bridges: B:K.16, B:E.31 GDP.8: 12 residues within 4Å: Chain C: G.15, K.16, S.17, A.18, F.28, D.30, E.31, Y.32, P.34, K.117 Chain E: R.102 Ligands: MG.7 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.13, C:G.15, C:K.16, C:S.17, C:A.18, C:Y.32, C:K.117, C:K.117, E:R.102 Salt bridges: C:K.16 GDP.10: 13 residues within 4Å: Chain D: A.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, E.31, Y.32, P.34, K.117 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:V.14, D:G.15, D:K.16, D:S.17, D:S.17, D:A.18, D:Y.32 Salt bridges: D:K.16 GDP.12: 15 residues within 4Å: Chain E: A.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, D.30, E.31, Y.32, P.34, K.117 Ligands: MG.11 9 PLIP interactions: 9 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:K.117 Salt bridges: E:K.16 GDP.14: 13 residues within 4Å: Chain F: A.11, V.12, G.13, V.14, G.15, K.16, S.17, D.30, E.31, Y.32, P.34, K.117 Ligands: MG.13 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:A.11, F:G.13, F:V.14, F:G.15, F:K.16, F:S.17 Salt bridges: F:K.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H.J. et al., Structural basis of the oncogenic KRAS mutant and GJ101 complex. Biochem.Biophys.Res.Commun. (2023)

Release Date

2022-12-07

Peptides

Isoform 2B of GTPase KRas: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
I

D
M

E
Q

F
U

Isoform 2B of GTPase KRas

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