SMTL ID : 6vjj.1

Crystal Structure of wild-type KRAS4b (GMPPNP-bound) in complex with RAS-binding domain (RBD) of RAF1/CRAF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.18, T.36 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 GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 25 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, A.60, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 25 PLIP interactions: 25 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:E.32, 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:S.18, A:D.34, A:Q.62, A:Q.62, A:K.148 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

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

CL.3: 2 residues within 4Å: Chain A: R.136, G.139 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: Q.44 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: Y.65, M.68 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: E.63, S.66, R.69, H.96, Q.100, R.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.66, A:R.69, A:R.69, A:H.96 EDO.8: 6 residues within 4Å: Chain B: C.45, A.46, V.47, R.60, L.61, W.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.47, B:V.47, B:R.60

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 4 residues within 4Å: Chain A: E.63, K.89, D.93, H.96 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.63, A:H.96 Hydrogen bonds: A:K.89, A:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, T.H. et al., KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation. Nat Commun (2021)

Release Date

2020-11-25

Peptides

GTPase KRas: A
RAF proto-oncogene serine/threonine-protein kinase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

RAF proto-oncogene serine/threonine-protein kinase

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