Research workbench
Crystal structure of human meizothrombin DESF1
Analyse Crystal structure of human meizothrombin DESF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E6P
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- DFK, NAG, NA, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 150 | 17% helix, 7% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
Ligands and binding sites
- DFK · D-phenylalanyl-N-[(1S)-4-{[(Z)-amino(imino)methyl]amino}-1-(chloroacetyl)butyl]-L-prolinamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, H
- NA · Sodium ion · metal · chains H
- SO4 · Sulfate ion · ion · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.70 | 0.87 | 27 | empty |
| 2 | 253 | 0.57 | 0.78 | 42 | DFK |
| 3 | 185 | 0.46 | 0.75 | 22 | empty |
| 4 | 159 | 0.45 | 0.75 | 24 | empty |
| 5 | 53 | 0.45 | 0.84 | 13 | empty |
Interfaces
1 interface between chains.
- L–H · 3032 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 3E6P · Crystal structure of human meizothrombin desF1 · the same entry in another collection · chain L against L, 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 3E6P · PDBe 3E6P · UniProt P00734
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