SMTL ID : 6p0i.1

Crystal structure of GDP-bound human RalA in a covalent complex with aryl sulfonyl fluoride compounds.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 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.6 22 PLIP interactions: 22 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:V.40, A:E.41, A:N.127, A:K.128, A:K.128, A:S.157, A:A.158, A:K.159 Water bridges: A:K.27, A:S.28, A:S.28 Salt bridges: A:K.27, A:D.130 pi-Stacking: A:F.39, A:F.39

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

EDO.2: 7 residues within 4Å: Chain A: F.34, K.53, V.55, V.56, R.161, D.165, F.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.53 Water bridges: A:R.161

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

ACT.3: 3 residues within 4Å: Chain A: N.150, N.152, R.178 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.152

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.79, Q.110, R.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:Q.110 Water bridges: A:D.74, A:D.74

1 x NL7: 4-[(5-methoxypyridin-3-yl)sulfamoyl]benzene-1-sulfonic acid(Covalent)

NL7.5: 12 residues within 4Å: Chain A: I.18, V.20, A.48, L.67, T.69, A.70, G.71, Q.72, E.73, R.79, Y.82, F.83 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.48, A:T.69, A:E.73, A:Y.82, A:Y.82 Hydrogen bonds: A:A.70, A:G.71, A:Q.72, A:E.73 Water bridges: A:R.79

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 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

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

CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: T.46, K.47, A.48 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: D.49, S.50 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 2 residues within 4Å: Chain A: N.144, E.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bum-Erdene, K. et al., Small-molecule covalent bond formation at tyrosine creates a binding site and inhibits activation of Ral GTPases. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-03-04

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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