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Ribosome inactivating protein type 1 from charybdis maritima agg

Analyse Ribosome inactivating protein type 1 from charybdis maritima agg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B7U
Type: protein
Length: 251 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Charybdin
EC: 3.2.2.22
UniProt: P84786
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Charybdin (EC 3.2.2.22)	protein	251	40% helix, 20% strand	P84786

Ligands and binding sites

MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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	107	0.44	0.78	22	empty
2	52	0.26	0.74	16	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2B7U · Ribosome inactivating protein type 1 from Charybdis maritima AGG · the same entry in another collection · chain A against A, TM-score 1.00
P84786 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein charybdin (P84786) · 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 P84786
Elsewhere: RCSB PDB 2B7U · PDBe 2B7U · UniProt P84786

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