MolNFT v1 · #159004 · protein

Ricin a chain bound to camelid

6OBC: “Ricin a chain bound to camelid”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.72). MolNFT v1 #159004 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OBC
Type: protein
Length: 378 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin a chain; Vhh antibody
EC: 3.2.2.22
UniProt: P02879
Ligands: CL
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ricin a chain (EC 3.2.2.22)	protein	259	41% helix, 22% strand	P02879
B	Vhh antibody	protein	119	5% helix, 55% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 3 copies · 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	436	0.72	0.82	56	empty
2	155	0.67	0.88	30	EDO
3	90	0.36	0.75	15	empty
4	51	0.25	0.73	21	empty

Interfaces

1 interface between chains.

A–B · 1052 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6OBC · Ricin A chain bound to camelid · 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 6OBC · PDBe 6OBC · UniProt P02879

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