SMTL ID : 6ob3.1 (1 other biounit)

Crystal structure of G13D-KRAS (GMPPNP-bound) in complex with GAP-related domain (GRD) of neurofibromin (NF1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 25 residues within 4Å: Chain A: A.12, G.13, D.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, P.35, T.36, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Chain B: R.69 Ligands: MG.2 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B Hydrogen bonds: 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:V.30, A:T.36, A:T.36, A:G.61, A:Q.62, A:Q.62, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148, B:R.69, B:R.69 Water bridges: A:S.18, A:S.18, A:K.148, A:K.148 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

CL.3: 4 residues within 4Å: Chain B: F.169, P.170, Q.171, N.172 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 3 residues within 4Å: Chain B: D.41, V.84, Y.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.41 MES.6: 3 residues within 4Å: Chain B: Q.48, W.51, Q.163 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.163 pi-Cation interactions: B:W.51 MES.7: 4 residues within 4Å: Chain B: Q.129, R.130, L.133, P.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.130

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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