Research workbench
Crystal structure of a nanobody raised against urokinase-type plasminogen activator
Analyse Crystal structure of a nanobody raised against urokinase-type plasminogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HDO
- Type
- protein
- Length
- 502 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HCV NS3/4A serine protease immoglobulin heavy chain
- UniProt
- A0A0F6YEF6
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-HCV NS3/4A serine protease immoglobulin heavy chain | protein | 126 | 5% helix, 45% strand | A0A0F6YEF6 |
| B | Anti-HCV NS3/4A serine protease immoglobulin heavy chain | protein | 127 | 5% helix, 46% strand | A0A0F6YEF6 |
| C | Anti-HCV NS3/4A serine protease immoglobulin heavy chain | protein | 125 | 2% helix, 47% strand | A0A0F6YEF6 |
| D | Anti-HCV NS3/4A serine protease immoglobulin heavy chain | protein | 124 | 5% helix, 48% strand | A0A0F6YEF6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains B, C, D
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 | 830 | 0.73 | 0.78 | 71 | empty |
| 2 | 106 | 0.45 | 0.79 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–C · 576 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 509 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 471 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 64 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5HDO · Crystal structure of a nanobody raised against urokinase-type plasminogen activator · 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 A0A0F6YEF6
- Elsewhere: RCSB PDB 5HDO · PDBe 5HDO · UniProt A0A0F6YEF6
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