MolNFT v1 · #56686 · protein
Crystal structure of a domain-swapped serpin dimer
2ZNH · Antithrombin-III: “Crystal structure of a domain-swapped serpin dimer”. X-ray diffraction, 2 ligands (NAG, MAN), 9 pockets (best druggability 0.80). MolNFT v1 #56686 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZNH
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III
- UniProt
- P01008
- Ligands
- NAG, MAN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antithrombin-III | protein | 408 | 30% helix, 33% strand | P01008 |
| B | Antithrombin-III | protein | 412 | 30% helix, 34% strand | P01008 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CIT · Citric acid · additive · 2 copies · chains B
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 | 1035 | 0.80 | 0.81 | 88 | empty |
| 2 | 250 | 0.67 | 0.83 | 38 | empty |
| 3 | 75 | 0.64 | 0.92 | 19 | empty |
| 4 | 162 | 0.59 | 0.82 | 22 | empty |
| 5 | 81 | 0.49 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 5627 Ų buried · 121 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 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 2ZNH · PDBe 2ZNH · UniProt P01008
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