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Crystal structure of antithrombin-III

Analyse Crystal structure of antithrombin-III in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B4X
Type: protein
Length: 823 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 · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	Antithrombin-III	protein	413	27% helix, 29% strand	P01008
L	Antithrombin-III	protein	410	26% helix, 30% strand	P01008

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	612	0.74	0.81	66	empty
2	134	0.56	0.82	27	empty
3	50	0.49	0.87	14	empty
4	150	0.45	0.76	25	empty
5	102	0.43	0.78	22	empty

Interfaces

1 interface between chains.

I–L · 932 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2B4X · Crystal Structure of Antithrombin-III · the same entry in another collection · chain L against L, TM-score 1.00
P01008 · AlphaFold monomer V2.0 prediction for antithrombin-III (P01008) · a predicted model of the same protein · chain I against A, TM-score 0.92

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 2B4X · PDBe 2B4X · UniProt P01008

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