SMTL ID : 9gtk.1 (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

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

EDO.1: 3 residues within 4Å: Chain A: E.3, K.5, E.76 Ligand excluded by PLIP EDO.2: 2 residues within 4Å: Chain A: D.30, Y.32 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: I.142, E.143, Q.150, G.151, D.154 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: R.41 Chain B: E.10, R.13 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: C.118, Q.150 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: F.28, D.30, E.31 Ligands: GNP.14 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: V.45, I.46, D.47, Y.157, R.161 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: I.21, Q.25, H.27, D.33 Chain B: K.80 Ligands: EDO.15 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: K.42, Q.43 Ligands: EDO.11 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: T.148, R.149, Q.150 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: I.24, Q.25, N.26 Ligands: EDO.9 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: I.21, T.35, I.36, Y.40 Chain B: H.79, K.80 Ligands: EDO.8 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: P.34 Chain B: R.112, N.146 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: E.51, E.54, V.55, K.58 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: N.64, G.93, A.94, D.95 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Ligands: 1PE.22 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: E.33 Ligands: PGE.23 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain B: L.4 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain A: S.17, D.57 Ligands: GNP.14 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.2, H2O.3 MG.13: 4 residues within 4Å: Chain A: S.39, Y.40, D.54 Chain B: W.36 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.40, H2O.7

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

GNP.14: 23 residues within 4Å: Chain A: A.11, 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.6, MG.12 22 PLIP interactions: 22 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:T.35, A:G.60, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: 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

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.22: 13 residues within 4Å: Chain A: R.41, D.54 Chain B: G.1, S.2, K.6, L.9, D.29, N.31, A.32, E.33, D.34, T.35 Ligands: EDO.19 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.6, B:E.33, B:T.35, A:R.41, A:D.54 Water bridges: B:D.29, B:N.31

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

PGE.23: 9 residues within 4Å: Chain B: E.33, T.35, W.36, G.37, A.65, S.66, D.67, A.68 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: 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
A

B
B

Isoform 2B of GTPase KRas

DARPin 784_F5

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