Research workbench
A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site
Analyse A novel serine protease inhibition motif involving a multi-centered short… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GHY
- Type
- protein
- Length
- 297 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Acetyl hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- 121, ZN, NA, CA
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin (EC 3.4.21.5) | protein | 36 | 28% helix, 0% strand | P00734 |
| H | Thrombin (EC 3.4.21.5) | protein | 250 | 13% helix, 35% strand | P00734 |
| I | Acetyl hirudin | protein | 11 | 27% helix, 0% strand | P28504 |
Ligands and binding sites
- 121 · 2-(3-hydroxy-pyridin-2-yl)-1H-benzoimidazole-5-carboxamidine · ligand · chains H
- ZN · Zinc ion · metal · 3 copies · chains L, H
- NA · Sodium ion · metal · chains H
- CA · Calcium 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 | 226 | 0.53 | 0.77 | 39 | ZN, 121 |
| 2 | 61 | 0.31 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1381 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 685 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1GHY · A novel serine protease inhibition motif involving a multi-centered short hydrogen… · the same entry in another collection · chain L against L, TM-score 1.00
- P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain I against A, TM-score 0.46
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 1GHY · PDBe 1GHY · UniProt P00734 · UniProt P28504
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