Research workbench
Crystal structure of P13 alanine variant of antithrombin
Analyse Crystal structure of P13 alanine variant of antithrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OYH
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III
- UniProt
- P01008
- Ligands
- NAG, MAN, BMA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Antithrombin-III | protein | 416 | 32% helix, 31% strand | P01008 |
| L | Antithrombin-III | protein | 410 | 29% helix, 31% strand | P01008 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains I, L
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.73 | 0.81 | 61 | empty |
| 2 | 89 | 0.55 | 0.85 | 18 | empty |
| 3 | 88 | 0.55 | 0.85 | 21 | empty |
| 4 | 66 | 0.53 | 0.86 | 17 | empty |
| 5 | 198 | 0.45 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- I–L · 936 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
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 1OYH · PDBe 1OYH · UniProt P01008
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