Research workbench
Human thrombin - inhibitor complex
Analyse Human thrombin - inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AZ2
- Type
- protein
- Length
- 298 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin-3A'
- EC
- 3.4.21.5
- UniProt
- P00734, P28509
- Ligands
- 9MU, NAG
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 33% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 257 | 14% helix, 34% strand | P00734 |
| D | Hirudin-3A' | protein | 11 | 0% helix, 0% strand | P28509 |
Ligands and binding sites
- 9MU · (R)-N-((S)-1-carbamimidoyl-piperidin-3-ylmethyl)-2-(naphthalene-2-sulfonylamino)-3-phenyl-propionamide · 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 | 248 | 0.55 | 0.77 | 39 | 9MU |
| 2 | 112 | 0.38 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1135 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 603 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
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
- Every structure of UniProt P28509
- Elsewhere: RCSB PDB 4AZ2 · PDBe 4AZ2 · UniProt P00734 · UniProt P28509
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