MolNFT v1 · #90160 · protein

Hyperstable in-frame insertion variant of antithrombin

4EB1 · Antithrombin-III: “Hyperstable in-frame insertion variant of antithrombin”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.74). MolNFT v1 #90160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4EB1
Type: protein
Length: 803 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antithrombin-III
UniProt: P01008
Ligands: NAG
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	Antithrombin-III	protein	411	31% helix, 35% strand	P01008
L	Antithrombin-III	protein	392	31% helix, 33% strand	P01008

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains I, L

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

Pockets

9 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	666	0.74	0.80	67	empty
2	56	0.62	0.93	17	empty
3	57	0.50	0.86	17	empty
4	57	0.49	0.85	18	empty
5	64	0.38	0.79	18	empty

Interfaces

1 interface between chains.

I–L · 834 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4EB1 · Hyperstable in-frame insertion variant of antithrombin · the same entry in another collection · chain I against I, TM-score 1.00
P01008 · AlphaFold monomer V2.0 prediction for antithrombin-III (P01008) · a predicted model of the same protein · chain L 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 P01008
Elsewhere: RCSB PDB 4EB1 · PDBe 4EB1 · UniProt P01008

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.