SMTL ID : 6pq3.1

Crystal structure of GDP-bound KRAS with ten residues long internal tandem duplication in the switch II region

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 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.127, K.128, D.130, L.131, S.156, A.157, K.158 Ligands: MG.2 19 PLIP interactions: 19 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.127, A:K.128, A:K.128, A:A.157, A:K.158 Water bridges: A:Y.33, A:A.60 Salt bridges: A:K.17, A:D.130 pi-Stacking: A:F.29, A:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.18 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

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

SO4.3: 5 residues within 4Å: Chain A: R.108, E.109, K.112, E.118, Y.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.109, A:E.118 Salt bridges: A:H.105, A:R.108, A:K.112 SO4.4: 2 residues within 4Å: Chain A: H.28, F.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.29 Water bridges: A:Q.23 Salt bridges: A:H.28 SO4.5: 3 residues within 4Å: Chain A: T.98, K.99, E.102 No protein-ligand interaction detected (PLIP) SO4.6: 5 residues within 4Å: Chain A: E.63, H.106, Q.110, R.113 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.110 Salt bridges: A:H.106, A:R.113 SO4.7: 7 residues within 4Å: Chain A: G.61, E.63, I.66, H.106, Y.107, Q.110 Ligands: SO4.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.61, A:E.63, A:E.63, A:Q.110 Salt bridges: A:H.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nelson, A.C. et al., RASinternal tandem duplication disrupts GTPase-activating protein (GAP) binding to activate oncogenic signaling. J.Biol.Chem. (2020)

Release Date

2020-05-20

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas