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Crystal structure of the rta-C10-P2 complex

Analyse Crystal structure of the rta-C10-P2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DDZ
Type: protein
Length: 265 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; 60S acidic ribosomal protein P2
EC: 3.2.2.22
UniProt: P02879, P05387
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin (EC 3.2.2.22)	protein	259	41% helix, 22% strand	P02879
B	60S acidic ribosomal protein P2	protein	6	50% helix, 0% strand	P05387

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	230	0.54	0.77	36	empty

Interfaces

1 interface between chains.

A–B · 412 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5DDZ · Crystal structure of the RTA-c10-P2 complex · the same entry in another collection · chain A against A, TM-score 1.00
P05387 · AlphaFold monomer V2.0 prediction for 60S acidic ribosomal protein P2 (P05387) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 P02879
Every structure of UniProt P05387
Elsewhere: RCSB PDB 5DDZ · PDBe 5DDZ · UniProt P02879 · UniProt P05387

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