Research workbench
The crystal structure of the Fab fragment of pro-upa antibody mab-112
Analyse The crystal structure of the Fab fragment of pro-upa antibody mab-112 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DVB
- Type
- protein
- Length
- 854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of pro-upa antibody mab-112
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Fab fragment of pro-upa antibody mab-112 | protein | 212 | 6% helix, 53% strand | — |
| B, L | Fab fragment of pro-upa antibody mab-112 | protein | 215 | 7% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, H, B, L
- PG4 · Tetraethylene glycol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.68 | 0.76 | 66 | PG4 |
| 2 | 770 | 0.68 | 0.76 | 68 | empty |
| 3 | 71 | 0.55 | 0.87 | 22 | empty |
| 4 | 101 | 0.52 | 0.83 | 23 | SO4 |
| 5 | 62 | 0.49 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1765 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1724 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 716 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4DVB · The crystal structure of the Fab fragment of pro-uPA antibody mAb-112 · 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
- Elsewhere: RCSB PDB 4DVB · PDBe 4DVB
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