Research workbench
Thrombin in complex with 3-amidinophenylalanine inhibitor
Analyse Thrombin in complex with 3-amidinophenylalanine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E7R
- Type
- protein
- Length
- 578 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- 0NW, NAG, NA, PO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 14% helix, 36% strand | P00734 |
| G | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 14% helix, 35% strand | P00734 |
| I, J | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
Ligands and binding sites
- 0NW · 3-[(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-{[(2',4'-dichlorobiphenyl-3-yl)sulfonyl]amino}-3-oxopropyl]benzenecarboximidamide · ligand · 2 copies · chains H, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H, G
- NA · Sodium ion · metal · 4 copies · chains H, G
- PO4 · Phosphate ion · ion · 2 copies · chains H, G
- GOL · Glycerol · additive · 3 copies · chains H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.59 | 0.77 | 42 | 0NW |
| 2 | 291 | 0.58 | 0.78 | 40 | 0NW |
| 3 | 54 | 0.29 | 0.75 | 15 | empty |
| 4 | 59 | 0.29 | 0.74 | 14 | GOL |
| 5 | 51 | 0.27 | 0.73 | 13 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1119 Ų buried · 27 hydrogen bonds · protein-protein
- M–G · 1112 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 641 Ų buried · 6 hydrogen bonds · protein-protein
- G–J · 617 Ų buried · 4 hydrogen bonds · protein-protein
- H–G · 412 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 4E7R · Thrombin in complex with 3-amidinophenylalanine inhibitor · 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
- Every structure of UniProt P09945
- Elsewhere: RCSB PDB 4E7R · PDBe 4E7R · UniProt P00734 · UniProt P09945
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.