MolNFT v1 · #135625 · protein

Rta-V1C7_G29R-high-salt

5U4L · Ricin: “Rta-V1C7_G29R-high-salt”. X-ray diffraction, 2 ligands (CL, PO4), 4 pockets (best druggability 0.55). MolNFT v1 #135625 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5U4L
Type: protein
Length: 386 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin; V1C7 vhh antibody G29R variant
EC: 3.2.2.22
UniProt: P02879
Ligands: CL, PO4
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin (EC 3.2.2.22)	protein	255	41% helix, 23% strand	P02879
B	V1C7 vhh antibody G29R variant	protein	131	9% helix, 48% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 5 copies · chains A
PO4 · Phosphate ion · ion · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A, B

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	220	0.55	0.78	30	empty
2	138	0.52	0.80	24	empty
3	64	0.42	0.81	17	PO4, EDO
4	55	0.33	0.76	12	empty

Interfaces

1 interface between chains.

A–B · 737 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5U4L · RTA-V1C7_G29R-high-salt · 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 5U4L · PDBe 5U4L · UniProt P02879

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