Research workbench
Complex of a divalent inhibitor with thrombin
Analyse Complex of a divalent inhibitor with thrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DIT
- Type
- protein
- Length
- 295 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Peptide inhibitor CVS995
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 2PP
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 251 | 16% helix, 37% strand | P00734 |
| P | Peptide inhibitor CVS995 | protein | 15 | 0% helix, 7% strand | — |
Ligands and binding sites
- 2PP · 2-propyl-pentanoic acid · ligand · chains H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.35 | 0.77 | 19 | empty |
| 2 | 59 | 0.28 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1200 Ų buried · 26 hydrogen bonds · protein-protein
- H–P · 1101 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 1DIT · Complex of a divalent inhibitor with thrombin · 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 1DIT · PDBe 1DIT · UniProt P00734
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