Research workbench
Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate
Analyse Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DEZ
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-phosphotyrosine antibody PY20-4D5 light chain; Anti-phosphotyrosine antibody…
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-phosphotyrosine antibody PY20-4D5 light chain | protein | 206 | 5% helix, 47% strand | — |
| H | Anti-phosphotyrosine antibody PY20-4D5 heavy chain | protein | 217 | 8% helix, 49% strand | — |
| A | Anti-phosphotyrosine antibody PY20-4D5 light chain | protein | 203 | 5% helix, 45% strand | — |
| B | Anti-phosphotyrosine antibody PY20-4D5 heavy chain | protein | 210 | 6% helix, 44% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.63 | 0.73 | 60 | empty |
| 2 | 512 | 0.59 | 0.74 | 65 | empty |
| 3 | 159 | 0.50 | 0.78 | 33 | empty |
| 4 | 213 | 0.46 | 0.74 | 25 | empty |
| 5 | 179 | 0.44 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1663 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1440 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 705 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6DEZ · Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate · the same entry in another collection · chain L against L, 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 6DEZ · PDBe 6DEZ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.