Research workbench
Thrombin inhibitor with a rigid tripeptidyl aldehydes
Analyse Thrombin inhibitor with a rigid tripeptidyl aldehydes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BA8
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0IT, NAG
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 30 | 27% helix, 0% strand | P00734 |
| B | Thrombin (EC 3.4.21.5) | protein | 252 | 13% helix, 36% strand | P00734 |
| C | Hirugen | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- 0IT · amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.58 | 0.77 | 45 | 0IT |
| 2 | 51 | 0.29 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1261 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 556 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, sulfation).
Compared structures
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 1BA8 · PDBe 1BA8 · UniProt P00734
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