SMTL ID : 6v6f.1

Crystal structure of Q61L KRAS(GMPPNP)-NF1(GRD)-SPRED1(EVH1) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: K.218 Chain B: M.68, Q.71 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.71, B:Q.71, A:K.218 FMT.2: 3 residues within 4Å: Chain A: E.201 Chain B: E.64, A.67 No protein-ligand interaction detected (PLIP) FMT.5: 2 residues within 4Å: Chain B: S.137, Y.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.98 FMT.7: 1 residues within 4Å: Chain C: R.98 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.98, C:R.98

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

GNP.3: 24 residues within 4Å: Chain B: 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, A.60, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.4 24 PLIP interactions: 22 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:S.18, B:S.18, B:A.19, B:V.30, B:T.36, B:T.36, B:G.61, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:S.18, B:T.36, A:K.235, A:K.235 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: H.230, D.251 Chain C: H.37, C.43 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:H.230, A:D.251, C:H.37, C:C.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, W. et al., Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR. Cell Rep (2020)

Release Date

2020-07-15

Peptides

Neurofibromin: A
GTPase KRas: B
Sprouty-related, EVH1 domain-containing protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Neurofibromin

GTPase KRas

Sprouty-related, EVH1 domain-containing protein 1

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