SMTL ID : 8dgt.1

Cryo-EM structure of a RAS/RAF complex (state 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-1-mer

Ligands

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

AGS.1: 20 residues within 4Å: Chain A: I.490, G.491, S.492, G.493, S.494, F.495, G.496, V.498, A.508, K.510, L.541, T.556, Q.557, W.558, C.559, K.605, N.608, F.610, D.621 Chain B: E.124 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.494, A:K.510, A:T.556, A:Q.557, A:C.559, A:N.608, A:D.621, B:E.124 Salt bridges: A:K.510, A:K.510, A:K.605 AGS.5: 21 residues within 4Å: Chain A: R.689 Chain B: L.96, G.97, A.98, G.99, N.100, V.104, A.117, K.119, M.165, E.166, S.172, Q.175, D.212, K.214, S.216, N.217, L.219, D.230 Ligands: MG.4, LCJ.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.100, B:E.166, B:M.168, B:S.172, B:D.212, B:S.216 Salt bridges: B:K.119, B:K.214

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: 4 residues within 4Å: Chain A: H.262, C.288, 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.4: 5 residues within 4Å: Chain B: K.119, S.216, N.217, D.230 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.230 MG.7: 5 residues within 4Å: Chain E: S.39, T.57, D.79, T.80 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: 16 residues within 4Å: Chain B: N.100, G.101, G.102, K.119, L.137, I.163, C.229, D.230, F.231, G.232, V.233, S.234, L.237, I.238, M.241 Ligands: AGS.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.100, B:V.233, B:S.234

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

GNP.8: 27 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, T.80, A.81, G.82, Q.83, N.138, K.139, D.141, L.142, S.167, A.168, K.169 Ligands: MG.7 20 PLIP interactions: 20 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:T.80, E:G.82, E:Q.83, 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

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
F

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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