Research workbench
Thrombin in complex with inhibitor
Analyse Thrombin in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GDE
- Type
- protein
- Length
- 286 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- SN3, NA
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 33% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 14% helix, 35% strand | P00734 |
| D | Hirudin | protein | 10 | 30% helix, 0% strand | P28504 |
Ligands and binding sites
- SN3 · (R)-3-((2S,3R)-1-((2s,3ar,5s,6s,7as)-2-(2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethylcarbamoyl)-5,6-dihydroxyocta hydro-1H-indol-1-yl)-3-chloro-4-methyl-1-oxopentan-2-ylamino)-2-methoxy-3-oxopropyl hydrogen sulfate · ligand · chains H
- NA · Sodium ion · metal · 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 | 288 | 0.55 | 0.76 | 38 | SN3 |
| 2 | 53 | 0.26 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1107 Ų buried · 25 hydrogen bonds · protein-protein
- H–D · 654 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
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 P28504
- Elsewhere: RCSB PDB 2GDE · PDBe 2GDE · UniProt P00734 · UniProt P28504
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