SMTL ID : 8ezg.1

Monobody 12D1 bound to KRAS(G12D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 15 residues within 4Å: Chain A: A.11, G.13, V.14, G.15, K.16, S.17, A.18, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:A.11, A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147 Water bridges: A:K.16, A:K.16, A:S.17, A:S.17, A:K.147, A:K.147 Salt bridges: A:K.16, A:D.119 pi-Cation interactions: A:K.117

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.17 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.1, H2O.2

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain B: S.20, W.21, S.54, T.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.20, B:W.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akkapeddi, P. et al., Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-07-19

Peptides

GTPase KRas: A
Monobody 12D1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

Monobody 12D1