MolNFT v1 · #5216 · protein
Complex structure of human thrombin with N-methyl-arginine inhibitor
1EB1 · Peptide inhibitor: “Complex structure of human thrombin with N-methyl-arginine inhibitor”. X-ray diffraction, 2 pockets (best druggability 0.39). MolNFT v1 #5216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EB1
- Type
- protein
- Length
- 297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide inhibitor; Thrombin heavy chain; Thrombin light chain…
- EC
- 3.4.21.5
- UniProt
- P00734
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide inhibitor | protein | 10 | 0% helix, 0% strand | — |
| H | Thrombin heavy chain | protein | 257 | 13% helix, 35% strand | P00734 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| B | 3-cyclohexyl-D-alanyl-L-prolyl-N~2~-methyl-L-arginine | protein | 3 | 0% helix, 33% strand | — |
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 | 78 | 0.39 | 0.78 | 21 | empty |
| 2 | 53 | 0.27 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1094 Ų buried · 27 hydrogen bonds · protein-protein
- A–H · 573 Ų buried · 4 hydrogen bonds · protein-protein
- H–B · 469 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 1EB1 · Complex structure of human thrombin with N-methyl-arginine inhibitor · the same entry in another collection · chain A against A, 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 1EB1 · PDBe 1EB1 · UniProt P00734
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