SMTL ID : 9gtk.3 (2 other biounits)

KRAS in complex with DARPin 784_F5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: F.28, E.31, K.147 Ligands: GNP.4 No protein-ligand interaction detected (PLIP) EDO.2: 5 residues within 4Å: Chain A: E.143, Q.150, G.151, D.154 Ligands: PGE.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.150, A:G.151

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.17, D.57 Ligands: GNP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.3 MG.6: 4 residues within 4Å: Chain A: S.39 Chain B: D.34, W.36, S.38 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.34, B:D.34, B:S.38, A:S.39

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

GNP.4: 22 residues within 4Å: Chain A: G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, A.59, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: EDO.1, MG.3 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:A.18, A:V.29, A:E.31, A:G.60, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:S.17, A:S.17, A:T.35, A:T.35 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28 pi-Cation interactions: A:K.117

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 5 residues within 4Å: Chain A: Q.131, F.141, I.142, E.143 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.143 PGE.7: 11 residues within 4Å: Chain A: M.67, Q.70, Y.71, T.74 Chain B: E.33, T.35, W.36, G.37, S.66, D.67, A.68 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.66, A:Q.70, A:T.74 Water bridges: B:S.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kapp, J.N. et al., A nucleotide-independent, pan-RAS-targeted DARPin elicits anti-tumor activity in a multimodal manner. Mol Oncol (2025)

Release Date

2025-06-25

Peptides

Isoform 2B of GTPase KRas: A
DARPin 784_F5: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

Isoform 2B of GTPase KRas

DARPin 784_F5

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