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Structure of ricin a chain bound with inhibitor 2,5-diamino- 4,6-dihydroxypyrimidine (ddp)

Analyse Structure of ricin a chain bound with inhibitor 2,5-diamino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IL5
Type: protein
Length: 531 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin a chain
EC: 3.2.2.22
UniProt: P02879
Ligands: DDP
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin a chain (EC 3.2.2.22)	protein	264	39% helix, 22% strand	P02879
B	Ricin a chain (EC 3.2.2.22)	protein	267	38% helix, 22% strand	P02879

Ligands and binding sites

DDP · 2,4-diamino-4,6-dihydroxypyrimidine · ligand · 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	286	0.56	0.76	33	DDP
2	236	0.55	0.78	31	empty
3	78	0.44	0.81	18	empty
4	98	0.43	0.78	14	empty
5	88	0.40	0.77	15	empty

Compared structures

1IL5 · Structure of ricin a chain bound with inhibitor 2,5-diamino-4,6-dihydroxypyrimidine (ddp) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt P02879
Elsewhere: RCSB PDB 1IL5 · PDBe 1IL5 · UniProt P02879

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