Research workbench
P14-fluorescein-N135Q-S380C-antithrombin-III
Analyse P14-fluorescein-N135Q-S380C-antithrombin-III in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DZH
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III
- UniProt
- P01008
- Ligands
- NAG, BMA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Antithrombin-III | protein | 418 | 31% helix, 30% strand | P01008 |
| L | Antithrombin-III | protein | 407 | 29% helix, 31% strand | P01008 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains I, L
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GOL · Glycerol · additive · 2 copies · chains I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.74 | 0.81 | 72 | empty |
| 2 | 70 | 0.63 | 0.91 | 19 | GOL |
| 3 | 135 | 0.62 | 0.85 | 25 | GOL |
| 4 | 248 | 0.54 | 0.76 | 35 | empty |
| 5 | 60 | 0.37 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- I–L · 928 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
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 1DZH · PDBe 1DZH · UniProt P01008
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