MolNFT v1 · #159006 · protein

Ricin a chain bound to vhh antibody V6H8

6OBE: “Ricin a chain bound to vhh antibody V6H8”. X-ray diffraction, 1 ligand (NI), 4 pockets (best druggability 0.72). MolNFT v1 #159006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OBE
Type: protein
Length: 382 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin a chain; Vhh antibody V6H8
EC: 3.2.2.22
UniProt: P02879
Ligands: NI
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin a chain (EC 3.2.2.22)	protein	265	40% helix, 21% strand	P02879
B	Vhh antibody V6H8	protein	117	5% helix, 56% strand	—

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
IMD · Imidazole · 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	504	0.72	0.82	52	empty
2	52	0.61	0.93	20	EDO
3	74	0.39	0.79	17	empty
4	51	0.26	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 1153 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6OBE · Ricin A chain bound to VHH antibody V6H8 · 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 6OBE · PDBe 6OBE · UniProt P02879

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