SMTL ID : 6wgn.3 (2 other biounits)

Crystal structure of K-Ras(G12D) GppNHp bound to cyclic peptide ligand KD2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 16 residues within 4Å: Chain A: D.12, G.13, V.14, G.15, K.16, S.17, A.18, A.59, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.12, A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:K.16, A:S.17, A:A.18, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:G.60, A:Q.61 Salt bridges: A:D.119

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., GTP-State-Selective Cyclic Peptide Ligands of K-Ras(G12D) Block Its Interaction with Raf. Acs Cent.Sci. (2020)

Release Date

2020-10-14

Peptides

GTPase KRas: A
Cyclic Peptide KD2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

GTPase KRas

Cyclic Peptide KD2

Related Entries With Identical Sequence