Research workbench
Thrombin-HIRUGEN_L-378,650
Analyse Thrombin-HIRUGEN_L-378,650 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MU8
- Type
- protein
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirudin iib
- EC
- 3.4.21.5
- UniProt
- P00734, P28506
- Ligands
- CDB
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| B | Thrombin (EC 3.4.21.5) | protein | 250 | 14% helix, 34% strand | P00734 |
| C | Hirudin iib | protein | 11 | 36% helix, 0% strand | P28506 |
Ligands and binding sites
- CDB · 2-(6-chloro-3-{[2,2-difluoro-2-(2-pyridinyl)ethyl]amino}-2-oxo-1(2H)-pyrazinyl)-N-[(2-fluoro-3-methyl-6-pyridinyl)methyl]acetamide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.55 | 0.77 | 40 | CDB |
Interfaces
2 interfaces between chains.
- A–B · 1112 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 684 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, sulfation).
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 P28506
- Elsewhere: RCSB PDB 1MU8 · PDBe 1MU8 · UniProt P00734 · UniProt P28506
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