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Crystal structure of native antithrombin in its monomeric form

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

PDB: 1T1F
Type: protein
Length: 1,257 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antithrombin-III
UniProt: P01008
Ligands: NAG, BMA, IOD
Pockets: 20 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Antithrombin-III	protein	419	30% helix, 28% strand	P01008

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C
BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C
IOD · Iodide ion · ion · 21 copies · chains A, B, C
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

20 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	59	0.64	0.93	18	empty
2	50	0.64	0.94	17	empty
3	50	0.63	0.94	14	empty
4	228	0.55	0.78	38	empty
5	146	0.52	0.80	34	IOD

Interfaces

2 interfaces between chains.

A–C · 452 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 440 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

1T1F · Crystal Structure of Native Antithrombin in its Monomeric Form · the same entry in another collection · chain A against A, TM-score 1.00
P01008 · AlphaFold monomer V2.0 prediction for antithrombin-III (P01008) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 1T1F · PDBe 1T1F · UniProt P01008

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