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Studies on crystal structures active center geometry and depurine mechanism of two ribosome-inactivating proteins

Analyse Studies on crystal structures active center geometry and depurine mechanism of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MRJ
Type: protein
Length: 247 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-trichosanthin
UniProt: P09989
Ligands: ADN
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-trichosanthin	protein	247	40% helix, 25% strand	P09989

Ligands and binding sites

ADN · Adenosine · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	150	0.47	0.77	22	ADN
2	76	0.34	0.75	15	empty

Compared structures

1MRJ · Studies on crystal structures active center geometry and depurine mechanism of two… · the same entry in another collection · chain A against A, TM-score 1.00
P09989 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein alpha-trichosanthin… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P09989
Elsewhere: RCSB PDB 1MRJ · PDBe 1MRJ · UniProt P09989

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