MolNFT v1 · #30649 · protein

Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator, ARF6

2A5F · ADP-ribosylation factor 6: “Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator, ARF6”. X-ray diffraction, 4 ligands (GTP, NAD, MG), 3 pockets (best druggability 0.60). MolNFT v1 #30649 on…

PDB: 2A5F
Type: protein
Length: 347 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylation factor 6; Cholera enterotoxin, a chain
EC: 2.4.2.36
UniProt: P62330, P01555
Ligands: GTP, NAD, MG, NA
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-ribosylation factor 6	protein	162	36% helix, 28% strand	P62330
B	Cholera enterotoxin, a chain (EC 2.4.2.36)	protein	185	34% helix, 24% strand	P01555

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A
NAD · Nicotinamide-adenine-dinucleotide · ligand · chains B
MG · Magnesium ion · metal · chains A
NA · Sodium ion · metal · chains B
GOL · Glycerol · additive · chains B

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

Pockets

3 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	339	0.60	0.77	40	NAD, GOL
2	189	0.53	0.78	30	empty
3	100	0.42	0.78	24	MG, GTP

Interfaces

1 interface between chains.

A–B · 929 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2A5F · Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator… · the same entry in another collection · chain B against B, TM-score 1.00
P62330 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 6 (P62330) · a predicted model of the same protein · chain A against A, TM-score 0.99
P01555 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit a (P01555) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 P62330
Every structure of UniProt P01555
Elsewhere: RCSB PDB 2A5F · PDBe 2A5F · UniProt P62330 · UniProt P01555

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