Research workbench
Intermediate structure of antithrombin bound to the natural pentasaccharide
Analyse Intermediate structure of antithrombin bound to the natural pentasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EVJ
- Type
- protein
- Length
- 821 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III
- UniProt
- P01008
- Ligands
- ZDO, SUS, NAG, MAN, IDS, BDP, SGN
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Antithrombin-III | protein | 404 | 29% helix, 27% strand | P01008 |
| L | Antithrombin-III | protein | 417 | 29% helix, 31% strand | P01008 |
Ligands and binding sites
- ZDO · methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside · ligand · 2 copies · chains I, L
- SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · 2 copies · chains I, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains I, L
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 2 copies · chains I, L
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains I, L
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.73 | 0.81 | 64 | empty |
| 2 | 93 | 0.61 | 0.88 | 24 | empty |
| 3 | 185 | 0.58 | 0.81 | 36 | empty |
| 4 | 123 | 0.58 | 0.84 | 24 | empty |
| 5 | 168 | 0.57 | 0.81 | 28 | empty |
Interfaces
1 interface between chains.
- I–L · 810 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3EVJ · Intermediate structure of antithrombin bound to the natural pentasaccharide · 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 3EVJ · PDBe 3EVJ · UniProt P01008
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