Research workbench
Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic peptide cyclotheonamide a
Analyse Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TMB
- Type
- protein
- Length
- 296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Hirugen; Cyclotheonamide a
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 252 | 16% helix, 35% strand | P00734 |
| I | Hirugen | protein | 10 | 30% helix, 0% strand | P09945 |
| T | Cyclotheonamide a | protein | 5 | 0% helix, 0% strand | — |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.29 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1227 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 623 Ų buried · 7 hydrogen bonds · protein-protein
- H–T · 541 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified, 1 d-amino (disulfide, nonstandard, D-amino acid, sulfation).
Compared structures
- 1TMB · Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic peptide… · the same entry in another collection · chain L against L, TM-score 1.00
- P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.58
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 1TMB · PDBe 1TMB · UniProt P00734 · UniProt P09945
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