Research workbench
Unliganded wild-type human thrombin
Analyse Unliganded wild-type human thrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U69
- Type
- protein
- Length
- 281 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
- BCN, NAG, NA, IOD, CL
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 30 | 43% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 251 | 16% helix, 36% strand | P00734 |
Ligands and binding sites
- BCN · Bicine · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · chains H
- IOD · Iodide ion · ion · chains H
- CL · Chloride ion · ion · chains H
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.57 | 0.78 | 40 | MPD |
| 2 | 89 | 0.33 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1224 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3U69 · Unliganded wild-type human thrombin · 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 3U69 · PDBe 3U69 · UniProt P00734
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