Research workbench
Thrombin-hirugen-GW420128 ternary complex at 1.39A resolution
Analyse Thrombin-hirugen-GW420128 ternary complex at 1.39A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UUK
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human alpha thrombin; Thrombin; Hirudin I
- EC
- 3.4.21.5
- UniProt
- P00734, P28501
- Ligands
- 897, NA, CA
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human alpha thrombin (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| B | Thrombin (EC 3.4.21.5) | protein | 252 | 15% helix, 34% strand | P00734 |
| H | Hirudin I | protein | 10 | 30% helix, 0% strand | P28501 |
Ligands and binding sites
- 897 · N-[3-(tert-butylamino)-3-oxopropyl]-N-isopropyl-3-methyl-5-{[(2S)-2-(pyridin-4-ylamino)propyl]oxy}benzamide · ligand · chains B
- NA · Sodium ion · metal · chains B
- CA · Calcium ion · metal · 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 | 285 | 0.59 | 0.78 | 45 | 897 |
Interfaces
2 interfaces between chains.
- A–B · 1124 Ų buried · 30 hydrogen bonds · protein-protein
- B–H · 618 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 2UUK · Thrombin-hirugen-gw420128 ternary complex at 1.39A resolution · 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 P28501
- Elsewhere: RCSB PDB 2UUK · PDBe 2UUK · UniProt P00734 · UniProt P28501
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