MolNFT v1 · #23000 · protein
Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms
1TMT · Alpha-thrombin (small subunit): “Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal…”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.32). MolNFT v1 #23000…
- PDB
- 1TMT
- 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); Cgp 50,856 inhibitor…
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 26 | 35% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 257 | 15% helix, 34% strand | P00734 |
| I | Cgp 50,856 inhibitor, cleaved N-terminal tripeptide fragment, D-phe-pro-arg | protein | 3 | 0% helix, 33% strand | — |
| J | Cgp 50,856 inhibitor, cleaved C-terminal hirudin fragment | protein | 10 | 0% helix, 0% strand | P28504 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 74 | 0.32 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1113 Ų buried · 23 hydrogen bonds · protein-protein
- H–J · 602 Ų buried · 6 hydrogen bonds · protein-protein
- H–I · 468 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 d-amino, 1 glycan (disulfide, D-amino acid, N-glycosylation).
Compared structures
- 1TMT · Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due… · 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 J against A, TM-score 0.53
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 1TMT · PDBe 1TMT · UniProt P00734 · UniProt P28504
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