MolNFT v1 · #122958 · protein

V5E1-rta complex

5J57 · Ricin: “V5E1-rta complex”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.57). MolNFT v1 #122958 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J57
Type: protein
Length: 388 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; Vhh single chain antibody V5E1
EC: 3.2.2.22
UniProt: P02879
Ligands: CL
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin (EC 3.2.2.22)	protein	264	39% helix, 22% strand	P02879
B	Vhh single chain antibody V5E1	protein	124	10% helix, 46% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 5 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.57	0.78	33	empty
2	86	0.48	0.82	20	empty
3	61	0.37	0.78	12	empty

Interfaces

1 interface between chains.

A–B · 621 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5J57 · V5E1-RTA complex · the same entry in another collection · 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 P02879
Elsewhere: RCSB PDB 5J57 · PDBe 5J57 · UniProt P02879

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