SMTL ID : 4g0n.1

Crystal Structure of wt H-Ras-GppNHp bound to the RBD of Raf Kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 24 residues within 4Å: Chain A: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:S.17, A:A.18, A:V.29, A:Y.32, A:T.35, A:T.35, A:G.60, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:D.33, A:T.35, A:Q.61 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 3 residues within 4Å: Chain A: D.107, Y.137 Ligands: ACT.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.107, A:Y.137, H2O.2, H2O.2, H2O.2 CA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.17, T.35, D.57 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.2, H2O.2

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 8 residues within 4Å: Chain A: R.97, S.106, D.107, D.108, V.109, M.111, Y.137 Ligands: CA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.109 Water bridges: A:D.107 Salt bridges: A:R.97

1 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.6: 5 residues within 4Å: Chain A: R.68, D.92, Q.95, Y.96, Q.99 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fetics, S.K. et al., Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD. Structure (2015)

Release Date

2013-07-17

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase HRas

RAF proto-oncogene serine/threonine-protein kinase

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