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Crystal structure of native S195A thrombin with an unoccupied active site
Analyse Crystal structure of native S195A thrombin with an unoccupied active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JOU
- Type
- protein
- Length
- 913 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin, light chain; Thrombin, heavy chain
- UniProt
- P00734
- Ligands
- NAG, NA
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin, light chain | protein | 45 | 27% helix, 0% strand | P00734 |
| B, F | Thrombin, heavy chain | protein | 259 | 15% helix, 34% strand | P00734 |
| C | Thrombin, light chain | protein | 47 | 23% helix, 0% strand | P00734 |
| D | Thrombin, heavy chain | protein | 257 | 14% helix, 32% strand | P00734 |
| E | Thrombin, light chain | protein | 46 | 24% helix, 0% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, F
- NA · Sodium ion · metal · 3 copies · chains B, D, F
- ACY · Acetic acid · additive · 5 copies · chains B, D, F
- GOL · Glycerol · additive · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.65 | 0.78 | 53 | ACY |
| 2 | 408 | 0.64 | 0.78 | 53 | ACY |
| 3 | 221 | 0.62 | 0.82 | 31 | empty |
| 4 | 266 | 0.56 | 0.77 | 37 | empty |
| 5 | 188 | 0.49 | 0.76 | 29 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1775 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1704 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1702 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 648 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 490 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1JOU · Crystal Structure of Native S195A Thrombin with an Unoccupied Active Site · 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 1JOU · PDBe 1JOU · UniProt P00734
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