SMTL ID : 8dgs.1

Cryo-EM structure of a RAS/RAF complex (state 1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-1-mer

Ligands

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Covalent)

AGS.1: 15 residues within 4Å: Chain A: G.493, S.494, F.495, V.498, A.508, K.510, L.541, Q.557, W.558, C.559, K.605, N.607, N.608, F.610, D.621 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.494, A:K.510, A:Q.557, A:C.559, A:N.608, A:D.621, A:D.621 Salt bridges: A:K.510, A:K.605 pi-Stacking: A:W.558, A:F.610, A:F.610 AGS.4: 17 residues within 4Å: Chain B: L.96, G.97, A.98, G.99, N.100, V.104, K.119, M.165, M.168, Q.175, K.214, S.216, N.217, L.219, D.230 Ligands: MG.5, LCJ.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.100, B:N.100, B:E.166, B:M.168, B:Q.175, B:K.214, B:K.214, B:S.216 Salt bridges: B:K.119

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.275, C.278, H.296, C.299 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.275, A:C.278, A:H.296, A:C.299 ZN.3: 5 residues within 4Å: Chain A: H.262, C.288, T.290, C.291, C.307 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.262, A:C.288, A:C.291, A:C.307

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain B: K.119, N.217, D.230 Ligands: AGS.4, LCJ.6 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain E: S.39, T.57 Ligands: GNP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.39, E:T.57

1 x LCJ: 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-6-carboxamide(Non-covalent)

LCJ.6: 15 residues within 4Å: Chain B: G.99, N.100, K.119, V.149, I.163, C.229, D.230, F.231, G.232, V.233, S.234, L.237, M.241 Ligands: AGS.4, MG.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.100, B:N.100, B:K.119, B:V.233, B:S.234 pi-Stacking: B:F.231 Halogen bonds: B:V.149

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

GNP.8: 25 residues within 4Å: Chain E: A.33, G.34, G.35, V.36, G.37, K.38, S.39, A.40, F.50, V.51, D.52, E.53, Y.54, P.56, T.57, A.81, G.82, N.138, K.139, D.141, L.142, S.167, A.168, K.169 Ligands: MG.7 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:G.35, E:V.36, E:G.37, E:K.38, E:K.38, E:S.39, E:A.40, E:E.53, E:T.57, E:T.57, E:G.82, E:N.138, E:K.139, E:K.139, E:A.168, E:K.169 Salt bridges: E:D.141 pi-Stacking: E:F.50, E:F.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, E. et al., Cryo-EM structure of a RAS/RAF recruitment complex. Nat Commun (2023)

Release Date

2023-07-05

Peptides

Serine/threonine-protein kinase B-raf: A
Dual specificity mitogen-activated protein kinase kinase 1: B
14-3-3 protein zeta: CD
GTPase KRas isoform X2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Serine/threonine-protein kinase B-raf

Dual specificity mitogen-activated protein kinase kinase 1

14-3-3 protein zeta

GTPase KRas isoform X2

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