Research workbench
Crystal structure of anti-upar Fab 8B12
Analyse Crystal structure of anti-upar Fab 8B12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QTH
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-upar antibody, heavy chain; Anti-upar antibody, light chain
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-upar antibody, heavy chain | protein | 224 | 9% helix, 51% strand | — |
| L | Anti-upar antibody, light chain | protein | 214 | 6% helix, 51% strand | — |
| A | Anti-upar antibody, heavy chain | protein | 215 | 6% helix, 52% strand | — |
| B | Anti-upar antibody, light chain | protein | 211 | 7% helix, 52% strand | — |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.58 | 0.74 | 70 | empty |
| 2 | 472 | 0.57 | 0.73 | 48 | empty |
| 3 | 112 | 0.52 | 0.82 | 21 | empty |
| 4 | 302 | 0.52 | 0.74 | 47 | empty |
| 5 | 53 | 0.35 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1887 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1670 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 402 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4QTH · Crystal structure of anti-uPAR Fab 8B12 · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 4QTH · PDBe 4QTH
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