MolNFT v1 · #4817 · protein
N135Q-S380C-antithrombin-III
1DZG: “N135Q-S380C-antithrombin-III”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.76). MolNFT v1 #4817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DZG
- Type
- protein
- Length
- 831 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III
- UniProt
- P01008
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Antithrombin-III | protein | 422 | 29% helix, 28% strand | P01008 |
| L | Antithrombin-III | protein | 409 | 28% helix, 31% strand | P01008 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains I, L
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.76 | 0.81 | 68 | empty |
| 2 | 53 | 0.69 | 0.97 | 20 | empty |
| 3 | 138 | 0.56 | 0.83 | 26 | GOL |
| 4 | 167 | 0.48 | 0.76 | 35 | empty |
| 5 | 50 | 0.43 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- I–L · 895 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
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 1DZG · PDBe 1DZG · UniProt P01008
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