SMTL ID : 8r7x.2 (1 other biounit)

Kras G12D in complex with compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

GCP.1: 27 residues within 4Å: Chain A: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, D.34, P.35, T.36, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.3 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:D.13, A:D.13, A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:S.18, A:A.19, A:V.30, A:D.31, A:Y.33, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:D.31, A:D.34, A:D.34, A:Q.62, A:Q.62, A:K.148 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

1 x YFJ: 8-pyridin-4-yl-2,3,4,9-tetrahydropyrido[3,4-b]indol-1-one

YFJ.2: 13 residues within 4Å: Chain A: E.4, K.6, L.7, V.8, S.40, Y.41, R.42, D.55, I.56, L.57, Y.72, T.75, G.76 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.8, A:R.42, A:D.55, A:L.57 Hydrogen bonds: A:R.42, A:T.75, A:T.75

1 x MG: MAGNESIUM ION

MG.3: 4 residues within 4Å: Chain A: K.17, S.18, T.36 Ligands: GCP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zak, K.M. et al., Kras G12D in complex with compound 4. To Be Published

Release Date

2024-10-02

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GTPase KRas

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