MolNFT v1 · #146357 · protein
Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine peptide
6DF2 · Anti-phosphotyrosine antibody C310-4D5 heavy chain: “Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine peptide”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #146357 on…
- PDB
- 6DF2
- Type
- protein
- Length
- 869 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-phosphotyrosine antibody C310-4D5 heavy chain; Anti-phosphotyrosine antibody…
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Anti-phosphotyrosine antibody C310-4D5 heavy chain | protein | 215 | 7% helix, 53% strand | — |
| H | Anti-phosphotyrosine antibody C310-4D5 light chain | protein | 219 | 8% helix, 51% strand | — |
| D, C | Leu-ptr-leu | protein | 3 | 0% helix, 0% strand | — |
| B | Anti-phosphotyrosine antibody C310-4D5 light chain | protein | 214 | 7% helix, 53% 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 | 873 | 0.76 | 0.80 | 96 | empty |
| 2 | 855 | 0.69 | 0.75 | 86 | empty |
| 3 | 188 | 0.56 | 0.80 | 37 | empty |
| 4 | 200 | 0.51 | 0.77 | 33 | empty |
| 5 | 73 | 0.34 | 0.77 | 17 | empty |
Interfaces
9 interfaces between chains.
- L–H · 1729 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1715 Ų buried · 14 hydrogen bonds · protein-protein
- H–B · 460 Ų buried · 5 hydrogen bonds · protein-protein
- H–D · 300 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 298 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, phosphorylation).
Compared structures
- 6DF2 · Improved anti-phosphotyrosine antibody 4G10-S5-4D5 Fab complexed with phosphotyrosine… · 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 6DF2 · PDBe 6DF2
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