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Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor
Analyse Crystal structure of the human alpha-thrombin-haemadin complex: an exosite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E0F
- Type
- protein
- Length
- 1,048 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Haemadin
- EC
- 3.4.21.5
- UniProt
- P00734, Q25163
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thrombin | protein | 36 | 25% helix, 0% strand | P00734 |
| C | Thrombin | protein | 35 | 31% helix, 0% strand | P00734 |
| D | Thrombin (EC 3.4.21.5) | protein | 257 | 13% helix, 35% strand | P00734 |
| E | Thrombin (EC 3.4.21.5) | protein | 256 | 12% helix, 36% strand | P00734 |
| F | Thrombin (EC 3.4.21.5) | protein | 259 | 15% helix, 35% strand | P00734 |
| I, K | Haemadin | protein | 57 | 0% helix, 16% strand | Q25163 |
| J | Haemadin | protein | 55 | 0% helix, 24% strand | Q25163 |
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.72 | 0.84 | 49 | empty |
| 2 | 124 | 0.55 | 0.83 | 19 | empty |
| 3 | 295 | 0.55 | 0.76 | 27 | empty |
| 4 | 195 | 0.50 | 0.77 | 36 | empty |
| 5 | 184 | 0.46 | 0.75 | 20 | empty |
Interfaces
13 interfaces between chains.
- C–F · 1347 Ų buried · 25 hydrogen bonds · protein-protein
- D–I · 1272 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1218 Ų buried · 25 hydrogen bonds · protein-protein
- F–K · 1197 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1184 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 1E0F · Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding… · 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
- Every structure of UniProt Q25163
- Elsewhere: RCSB PDB 1E0F · PDBe 1E0F · UniProt P00734 · UniProt Q25163
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