SMTL ID : 5whe.1 (3 other biounits)

KRas G12V/D38P, bound to GppNHp and miniprotein 225-11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

hetero-1-2-mer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 17 residues within 4Å: Chain A: V.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, G.64, N.120, K.121, D.123, L.124, S.149, A.150, K.151 Ligands: MG.6 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.17, A:V.18, A:G.19, A:K.20, A:K.20, A:S.21, A:A.22, A:G.64, A:N.120, A:K.121, A:K.121, A:A.150, A:K.151 Water bridges: A:S.21, A:S.21, A:S.21, A:S.21 Salt bridges: A:D.123 pi-Stacking: A:F.32, A:F.32

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 1 residues within 4Å: Chain A: Q.29 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:Q.29, H2O.1, H2O.2, H2O.4, H2O.4 CA.3: 2 residues within 4Å: Chain A: E.67 Chain B: A.35 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.67, A:E.67, B:A.35, H2O.3 CA.4: 2 residues within 4Å: Chain A: E.67, Y.68 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.67, A:Y.68, H2O.3, H2O.4 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: S.21 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.21, H2O.1, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGee, J.H. et al., Exceptionally high-affinity Ras binders that remodel its effector domain. J. Biol. Chem. (2018)

Release Date

2018-01-03

Peptides

GTPase KRas: A
Miniprotein 225-11: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTPase KRas

Miniprotein 225-11

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