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ANTITHROMBIN/PENTASACCHARIDE complex

Analyse ANTITHROMBIN/PENTASACCHARIDE complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1AZX
Type: protein
Length: 831 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antithrombin
UniProt: P01008
Ligands: Z9L, Z9K, GU6, GU1, Z9H, NAG
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	Antithrombin	protein	417	33% helix, 28% strand	P01008
L	Antithrombin	protein	414	29% helix, 31% strand	P01008

Ligands and binding sites

Z9L · methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside · ligand · 2 copies · chains I, L
Z9K · 3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid · ligand · 2 copies · chains I, L
GU6 · 2,3,6-tri-O-sulfo-alpha-D-glucopyranose · ligand · 2 copies · chains I, L
GU1 · 2,3-di-O-methyl-beta-D-glucopyranuronic acid · ligand · 2 copies · chains I, L
Z9H · 3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose · ligand · 2 copies · chains I, L
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains I, L

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	407	0.74	0.84	37	empty
2	73	0.63	0.91	19	empty
3	401	0.59	0.75	45	empty
4	289	0.58	0.77	36	empty
5	144	0.57	0.82	20	empty

Interfaces

1 interface between chains.

I–L · 260 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

1AZX · ANTITHROMBIN/PENTASACCHARIDE complex · 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 I against A, TM-score 0.95

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 1AZX · PDBe 1AZX · UniProt P01008

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