MolNFT v1 · #106996 · protein

Crystal structure of dioscorin complexed with ascorbate

4TWL · Dioscorin 5: “Crystal structure of dioscorin complexed with ascorbate”. X-ray diffraction, 2 ligands (ASC, SO4), 4 pockets (best druggability 0.70). MolNFT v1 #106996 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4TWL
Type: protein
Length: 475 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dioscorin 5
UniProt: A7MAQ2
Ligands: ASC, SO4
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dioscorin 5	protein	239	19% helix, 37% strand	A7MAQ2
B	Dioscorin 5	protein	236	19% helix, 36% strand	A7MAQ2

Ligands and binding sites

ASC · Ascorbic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 5 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	611	0.70	0.78	54	empty
2	155	0.54	0.80	21	ASC
3	123	0.51	0.81	21	ASC
4	179	0.45	0.75	33	empty

Interfaces

1 interface between chains.

A–B · 479 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4TWL · Crystal structure of dioscorin complexed with ascorbate · the same entry in another collection · chain A against A, TM-score 1.00
A7MAQ2 · AlphaFold monomer V2.0 prediction for dioscorin DIOA3 (A7MAQ2) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 A7MAQ2
Elsewhere: RCSB PDB 4TWL · PDBe 4TWL · UniProt A7MAQ2

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