SMTL ID : 5xco.1

Crystal structure of human K-Ras G12D Mutant in complex with GDP and Cyclic Inhibitory Peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-1-1-mer

Ligands

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

GDP.1: 18 residues within 4Å: Chain A: D.14, G.15, V.16, G.17, K.18, S.19, A.20, F.30, V.31, D.32, T.37, N.118, K.119, D.121, L.122, S.147, A.148, K.149 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.15, A:V.16, A:G.17, A:K.18, A:S.19, A:A.20, A:V.31, A:D.32, A:T.37, A:T.37, A:N.118, A:K.119, A:K.119, A:A.148, A:K.149 Water bridges: A:K.18, A:K.18, A:K.18, A:E.33, A:T.37, A:T.37, A:T.37, A:T.37, A:K.149 Salt bridges: A:K.18, A:D.121 pi-Stacking: A:F.30, A:F.30

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: F.92, E.93, I.95, H.96, L.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sogabe, S. et al., Crystal Structure of a Human K-Ras G12D Mutant in Complex with GDP and the Cyclic Inhibitory Peptide KRpep-2d. ACS Med Chem Lett (2017)

Release Date

2017-05-24

Peptides

GTPase KRas: A
ACE-ARG-ARG-ARG-ARG-CYS-PRO-LEU-TYR-ILE-SER-TYR-ASP-PRO-VAL-CYS-ARG-ARG-ARG-ARG-NH2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

ACE-ARG-ARG-ARG-ARG-CYS-PRO-LEU-TYR-ILE-SER-TYR-ASP-PRO-VAL-CYS-ARG-ARG-ARG-ARG-NH2