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Crystal structure of the ral-binding domain of EXO84 in complex with the active rala

Analyse Crystal structure of the ral-binding domain of EXO84 in complex with the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZC3
Type: protein
Length: 564 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein ral-a; Exocyst complex protein EXO84
UniProt: P11233, O54924
Ligands: GNP, MG
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RAS-related protein ral-a	protein	173	41% helix, 25% strand	P11233
B, D	Exocyst complex protein EXO84	protein	109	19% helix, 51% strand	O54924

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.63	0.81	33	MG, GNP
2	170	0.57	0.81	18	empty
3	156	0.56	0.82	29	MG, GNP
4	70	0.49	0.84	21	empty
5	72	0.48	0.83	23	empty

Interfaces

3 interfaces between chains.

B–C · 969 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 966 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 663 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1ZC3 · Crystal structure of the Ral-binding domain of Exo84 in complex with the active RalA · the same entry in another collection · chain A against A, TM-score 1.00
P11233 · AlphaFold monomer V2.0 prediction for RAS-related protein ral-a (P11233) · a predicted model of the same protein · chain A against A, TM-score 0.99
O54924 · AlphaFold monomer V2.0 prediction for exocyst complex component 8 (O54924) · a predicted model of the same protein · chain D against A, TM-score 0.88

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P11233
Every structure of UniProt O54924
Elsewhere: RCSB PDB 1ZC3 · PDBe 1ZC3 · UniProt P11233 · UniProt O54924

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