MolNFT v1 · #122957 · protein

RTA-V1C7

5J56 · Ricin: “RTA-V1C7”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.57). MolNFT v1 #122957 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J56
Type: protein
Length: 383 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; Vhh single chain antibody V1C7
EC: 3.2.2.22
UniProt: P02879
Ligands: CL
Pockets: 4 · 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	254	41% helix, 22% strand	P02879
B	Vhh single chain antibody V1C7	protein	129	9% helix, 46% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A
ACY · Acetic acid · additive · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

4 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	278	0.57	0.77	35	CL
2	161	0.51	0.78	21	ACY
3	51	0.36	0.80	18	CL
4	54	0.32	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 763 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5J56 · RTA-V1C7 · 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 5J56 · PDBe 5J56 · UniProt P02879

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