SMTL ID : 5wpm.1

KRas G12V, bound to GppNHp and miniprotein 225-11(A30R)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-2-mer

Ligands

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

GNP.1: 20 residues within 4Å: Chain A: A.11, V.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:A.18, A:G.60, A:Q.61, A:Q.61, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147, A:K.147 Water bridges: A:S.17, A:S.17, A:S.17, A:S.17, A:D.57, B:R.30 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.17 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.1 MG.3: 7 residues within 4Å: Chain A: G.10, A.11, V.81, F.82, S.89, I.93, Y.96 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.81, A:S.89

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

SO4.4: 4 residues within 4Å: Chain C: R.3, P.5, R.6, R.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.6 Salt bridges: C:R.3, C:R.6, C:R.23

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
Ras binding peptide: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTPase KRas

Ras binding peptide

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