Research workbench
Structure of serine proteinase
Analyse Structure of serine proteinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TOC
- Type
- protein
- Length
- 1,628 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Ornithodorin
- EC
- 3.4.21.5
- UniProt
- P00735, P56409
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Thrombin (EC 3.4.21.5) | protein | 28 | 39% helix, 0% strand | P00735 |
| B, D, F, H | Thrombin (EC 3.4.21.5) | protein | 259 | 12% helix, 32% strand | P00735 |
| R, S, T, U | Ornithodorin | protein | 120 | 18% helix, 31% strand | P56409 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.77 | 0.80 | 92 | empty |
| 2 | 951 | 0.75 | 0.78 | 86 | empty |
| 3 | 216 | 0.67 | 0.85 | 38 | empty |
| 4 | 232 | 0.60 | 0.80 | 35 | empty |
| 5 | 194 | 0.56 | 0.80 | 35 | empty |
Interfaces
17 interfaces between chains.
- B–R · 1855 Ų buried · 35 hydrogen bonds · protein-protein
- F–T · 1850 Ų buried · 40 hydrogen bonds · protein-protein
- D–S · 1812 Ų buried · 34 hydrogen bonds · protein-protein
- H–U · 1795 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 1197 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 1TOC · Structure of serine proteinase · the same entry in another collection · chain U against U, 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 P00735
- Every structure of UniProt P56409
- Elsewhere: RCSB PDB 1TOC · PDBe 1TOC · UniProt P00735 · UniProt P56409
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