Research workbench
Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric unit)
Analyse Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HK6
- Type
- protein
- Length
- 602 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P19221
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thrombin light chain (EC 3.4.21.5) | protein | 43 | 35% helix, 0% strand | P19221 |
| B, D | Thrombin heavy chain (EC 3.4.21.5) | protein | 258 | 14% helix, 32% strand | P19221 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.83 | 0.84 | 94 | empty |
| 2 | 204 | 0.53 | 0.78 | 30 | empty |
| 3 | 54 | 0.51 | 0.87 | 17 | empty |
| 4 | 155 | 0.49 | 0.78 | 23 | empty |
| 5 | 69 | 0.42 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1688 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1678 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1288 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3HK6 · Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric… · the same entry in another collection · chain A against A, TM-score 1.00
- P19221 · AlphaFold monomer V2.0 prediction for prothrombin (P19221) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P19221
- Elsewhere: RCSB PDB 3HK6 · PDBe 3HK6 · UniProt P19221
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