MolNFT v1 · #3872 · protein

Guanine nucleotide dissociation inhibitor, alpha-isoform

1D5T: “Guanine nucleotide dissociation inhibitor, alpha-isoform”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.56). MolNFT v1 #3872 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1D5T
Type: protein
Length: 433 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide dissociation inhibitor
UniProt: P21856
Ligands: SO4
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide dissociation inhibitor	protein	433	34% helix, 24% strand	P21856

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.56	0.84	24	empty
2	95	0.54	0.84	27	empty
3	143	0.47	0.78	25	empty
4	84	0.42	0.79	23	SO4
5	53	0.36	0.80	14	empty

Compared structures

1D5T · Guanine nucleotide dissociation inhibitor, alpha-isoform · 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 0.97

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 1D5T · PDBe 1D5T · UniProt P21856

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