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Crystal structure of the rab effector guanine nucleotide dissociation inhibitor (gdi) in complex with a geranylgeranyl (gg) peptide

Analyse Crystal structure of the rab effector guanine nucleotide dissociation inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LV0
Type: protein
Length: 433 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rab GDP disossociation inhibitor alpha
UniProt: P21856
Ligands: GER, SO4
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rab GDP disossociation inhibitor alpha	protein	433	36% helix, 25% strand	P21856

Ligands and binding sites

GER · Geran-8-yl geran · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.51	0.84	20	empty
2	132	0.47	0.78	23	SO4
3	147	0.45	0.76	24	empty
4	57	0.38	0.80	13	empty
5	63	0.30	0.74	17	empty

Compared structures

1LV0 · Crystal structure of the Rab effector guanine nucleotide dissociation inhibitor (GDI) in… · the same entry in another collection · chain A against A, TM-score 1.00
P21856 · AlphaFold monomer V2.0 prediction for rab GDP dissociation inhibitor alpha (P21856) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P21856
Elsewhere: RCSB PDB 1LV0 · PDBe 1LV0 · UniProt P21856

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