Research workbench
1.6 a structure of the pci-thrombin-heparin complex
Analyse 1.6 a structure of the pci-thrombin-heparin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B9F
- Type
- protein
- Length
- 653 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Plasma serine protease inhibitor
- EC
- 3.4.21.5
- UniProt
- P00734, P05154
- Ligands
- NAG, FUC, SGN, IDS, SO4
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 44 | 32% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 253 | 14% helix, 34% strand | P00734 |
| I | Plasma serine protease inhibitor | protein | 356 | 29% helix, 34% strand | P05154 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- FUC · alpha-L-fucopyranose · sugar · chains I
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains H
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains H
- SO4 · Sulfate ion · ion · 3 copies · chains H, I
- GOL · Glycerol · additive · 5 copies · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.54 | 0.74 | 41 | GOL |
| 2 | 158 | 0.52 | 0.79 | 31 | empty |
| 3 | 82 | 0.40 | 0.77 | 18 | empty |
| 4 | 95 | 0.35 | 0.74 | 15 | GOL |
| 5 | 97 | 0.35 | 0.74 | 24 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1759 Ų buried · 40 hydrogen bonds · protein-protein
- H–I · 1088 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 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 P00734
- Every structure of UniProt P05154
- Elsewhere: RCSB PDB 3B9F · PDBe 3B9F · UniProt P00734 · UniProt P05154
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