SMTL ID : 8ebz.1

Crystal Structure of GMPPNP-bound KRAS-G13D mutant at 1.2 Ang resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

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

GNP.1: 22 residues within 4Å: Chain A: A.12, G.13, D.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2, MG.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:D.14, A:D.14, A:D.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:A.19, A:D.31, A:G.61, A:Q.62, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:D.31 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.18 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.18, H2O.2, H2O.3, H2O.4 MG.3: 2 residues within 4Å: Chain A: Q.62 Ligands: GNP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: G.139 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.139, H2O.1, H2O.2, H2O.4, H2O.6 MG.5: 1 residues within 4Å: Chain A: D.120 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.120, H2O.5, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chao, F.A. et al., Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D . Commun Biol (2023)

Release Date

2023-06-07

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2B of GTPase KRas

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