MolNFT v1 · #21616 · protein
Crystal structure of the procoagulant fast form of thrombin
1SG8: “Crystal structure of the procoagulant fast form of thrombin”. X-ray diffraction, 2 ligands (NAG, NA), 9 pockets (best druggability 0.63). MolNFT v1 #21616 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SG8
- Type
- protein
- Length
- 556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG, NA
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Thrombin | protein | 27 | 33% helix, 0% strand | P00734 |
| B, E | Thrombin (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
- NA · Sodium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.63 | 0.78 | 56 | empty |
| 2 | 257 | 0.56 | 0.77 | 41 | empty |
| 3 | 149 | 0.53 | 0.80 | 30 | empty |
| 4 | 89 | 0.38 | 0.76 | 24 | empty |
| 5 | 87 | 0.38 | 0.77 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1112 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1095 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 377 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1SG8 · Crystal structure of the procoagulant fast form of thrombin · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 1SG8 · PDBe 1SG8 · UniProt P00734
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