SMTL ID : 8f0m.1 (1 other biounit)

Monobody 12D5 bound to KRAS(G12D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.19 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.19, H2O.1, H2O.1, H2O.1, H2O.1

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

GDP.2: 16 residues within 4Å: Chain A: A.13, G.15, V.16, G.17, K.18, S.19, A.20, F.30, N.118, K.119, D.121, L.122, S.147, A.148, K.149 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.13, A:G.15, A:V.16, A:G.17, A:K.18, A:S.19, A:A.20, A:N.118, A:K.119, A:K.119, A:A.148, A:K.149 Water bridges: A:D.14, A:S.19, A:S.19, A:S.19 Salt bridges: A:K.18, A:D.121 pi-Stacking: A:F.30, A:F.30

2 x GLC: alpha-D-glucopyranose(Non-functional Binders)(Non-covalent)

GLC.3: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.89, A:T.89, A:T.89 GLC.4: 5 residues within 4Å: Chain B: Y.37, F.49, T.59, I.60, S.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.61, B:S.61

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

Isoform 2B of GTPase KRas: A
Monobody 12D5: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 2B of GTPase KRas

Monobody 12D5

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