Research workbench
D-phe-pro-arg-type thrombin inhibitor
Analyse D-phe-pro-arg-type thrombin inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NZQ
- Type
- protein
- Length
- 288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Decapeptide hirudin analogue
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 162
- Pockets
- 3 · best druggability 0.57
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 | 28 | 21% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 15% helix, 34% strand | P00734 |
| D | Decapeptide hirudin analogue | protein | 10 | 30% helix, 0% strand | — |
Ligands and binding sites
- 162 · (2-{2-[(5-carbamimidoyl-1-methyl-1H-pyrrol-3-ylmethyl)-carbamoyl]-pyrrol-1-yl} -1-cyclohexylmethyl-2-oxo-ethylamino)-acetic acid · ligand · chains H
- SIN · Succinic acid · additive · chains H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.57 | 0.77 | 40 | 162 |
| 2 | 56 | 0.32 | 0.76 | 19 | empty |
| 3 | 56 | 0.30 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1115 Ų buried · 28 hydrogen bonds · protein-protein
- H–D · 658 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 modified, 1 covalent (disulfide, nonstandard, additive adduct, hydroxylation).
Compared structures
- 1NZQ · D-Phe-Pro-Arg-Type Thrombin 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
- Elsewhere: RCSB PDB 1NZQ · PDBe 1NZQ · UniProt P00734
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