SMTL ID : 6ob2.1 (1 other biounit)

Crystal structure of wild-type KRAS (GMPPNP-bound) in complex with GAP-related domain (GRD) of neurofibromin (NF1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: D.154, D.155, Y.158, R.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.155, A:R.162, A:R.162 GOL.4: 9 residues within 4Å: Chain A: A.67, M.68, Q.71 Chain B: V.191, S.192, E.195, K.202, E.208, K.212 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.192, B:K.202, B:E.208, B:E.208, B:K.212, A:Q.71

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

GNP.2: 24 residues within 4Å: Chain A: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:A.19, A:V.30, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:Y.33, A:Q.62, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.18, T.36, D.58 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.1

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 1 residues within 4Å: Chain B: Y.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.194 pi-Stacking: B:Y.194

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rabara, D. et al., KRAS G13D sensitivity to neurofibromin-mediated GTP hydrolysis. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-10-16

Peptides

GTPase KRas: A
Neurofibromin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

Neurofibromin

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