SMTL ID : 9gtk.2 (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

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

EDO.1: 6 residues within 4Å: Chain A: E.143, Q.150, G.151, D.154 Ligands: EDO.2, PGE.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.150 EDO.2: 5 residues within 4Å: Chain A: Q.131, F.141, I.142, E.143 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.131, A:E.143 EDO.3: 3 residues within 4Å: Chain A: C.118, E.143, Q.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.143, A:Q.150 EDO.4: 2 residues within 4Å: Chain A: D.119, T.148 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.119, A:D.119 EDO.5: 4 residues within 4Å: Chain A: M.1, T.2, E.3, K.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.1, A:E.3, A:K.167, A:K.167 EDO.6: 5 residues within 4Å: Chain A: I.21, Q.25, V.29, D.33, T.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.25 Water bridges: A:Y.40 EDO.7: 4 residues within 4Å: Chain A: Q.131, A.134, R.135, I.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.135 Water bridges: A:Q.131, A:F.141 EDO.8: 2 residues within 4Å: Chain A: Q.25, H.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.27 Water bridges: A:Q.25 EDO.9: 4 residues within 4Å: Chain A: R.41, Q.43 Chain B: R.13 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.43 EDO.14: 3 residues within 4Å: Chain B: R.13, T.47 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.13

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain A: S.17, D.57 Ligands: GNP.11 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.2 MG.15: 5 residues within 4Å: Chain A: S.39, Y.40, D.54 Chain B: D.34, W.36 No protein-ligand interaction detected (PLIP)

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

GNP.11: 19 residues within 4Å: Chain A: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, E.31, A.59, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.10 21 PLIP interactions: 21 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:S.17, A:A.18, A:A.59, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:V.29, A:D.30 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28

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

PGE.12: 7 residues within 4Å: Chain A: R.149, Q.150, G.151, V.152, D.153, D.154 Ligands: EDO.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.151, A:D.153, A:D.154 Water bridges: A:V.152, A:D.153

1 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.13: 5 residues within 4Å: Chain A: R.97, K.101, E.107, S.136, Y.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.101 Salt bridges: A:R.97, A:K.101

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
C

B
I

Isoform 2B of GTPase KRas

DARPin 784_F5

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