SMTL ID : 8fjh.1

Crystal structure of RalA in a covalent complex with SOF-531

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 residues within 4Å: Chain A: S.22, G.23, G.24, V.25, G.26, K.27, S.28, A.29, F.39, V.40, E.41, Y.43, N.127, K.128, D.130, L.131, S.157, A.158, K.159 Ligands: CA.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.22, A:G.24, A:V.25, A:G.26, A:K.27, A:S.28, A:A.29, A:E.41, A:E.41, A:Y.43, A:N.127, A:K.128, A:K.128, A:S.157, A:A.158, A:K.159 Water bridges: A:S.22, A:K.27, A:Y.43 Salt bridges: A:K.27, A:D.130 pi-Stacking: A:F.39, A:F.39

1 x Y0P: 8-[bis(oxidanyl)-$l^{3}-sulfanyl]-~{N}-(3-fluoranyl-5-methoxy-phenyl)-2,3-dihydro-1,4-benzodioxine-5-sulfonamide(Covalent)

Y0P.2: 14 residues within 4Å: Chain A: V.20, G.21, A.48, L.67, T.69, A.70, G.71, Q.72, E.73, I.78, R.79, Y.82, F.83, F.107 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.48, A:R.79, A:Y.82, A:Y.82, A:F.83 Hydrogen bonds: A:A.70, A:G.71, A:Q.72, A:E.73, A:E.73 Water bridges: A:A.48, A:R.79

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: K.27, S.28, Y.43, P.45 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.28, H2O.2, H2O.2, H2O.2, H2O.3 CA.4: 3 residues within 4Å: Chain A: L.14, H.15, E.87 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:L.14, H2O.5, H2O.5, H2O.6, H2O.7 CA.5: 3 residues within 4Å: Chain A: D.37, K.53, R.161 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Landgraf, A.D. et al., Exploring Covalent Bond Formation at Tyr-82 for Inhibition of Ral GTPase Activation. Chemmedchem (2023)

Release Date

2023-12-06

Peptides

Ras-related protein Ral-A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ras-related protein Ral-A

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