SMTL ID : 7acf.2 (1 other biounit)

CRYSTAL STRUCTURE OF CRYSTAL FORM 2 OF AN ACTIVE KRAS G12D (GPPCP) DIMER IN COMPLEX WITH BI-5747

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.18, T.36 Ligands: GCP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: S.18, T.36 Ligands: GCP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.4, H2O.5

2 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.2: 25 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, P.35, T.36, A.60, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.13, A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:A.19, A:V.30, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 GCP.5: 25 residues within 4Å: Chain B: 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, P.35, T.36, T.59, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:S.18, B:A.19, B:V.30, B:T.36, B:T.36, B:G.61, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:S.18, B:S.18, B:Y.33, B:D.34 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

1 x R6W: (3~{S})-5-oxidanyl-3-[2-[[6-[[3-[(1~{S})-6-oxidanyl-3-oxidanylidene-1,2-dihydroisoindol-1-yl]-1~{H}-indol-2-yl]methylamino]hexylamino]methyl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one(Non-covalent)

R6W.3: 16 residues within 4Å: Chain A: M.2, E.4, K.6, L.7, V.8, E.38, S.40, R.42, L.53, D.55, L.57, M.68, Q.71, Y.72, T.75, G.76 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.6, A:K.6, A:V.8, A:L.57, A:Q.71, A:Y.72 Hydrogen bonds: A:E.4, A:E.4, A:E.4, A:D.55, A:D.55, A:M.68 Water bridges: A:E.4 pi-Cation interactions: A:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kessler, D. et al., Reply to Tran et al.: Dimeric KRAS protein-protein interaction stabilizers. Proc. Natl. Acad. Sci. U.S.A. (2020)

Release Date

2020-11-18

Peptides

GTPase KRas: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

GTPase KRas

Related Entries With Identical Sequence