Research workbench
Crystal structure of engineered anti-ee scfv antibody fragment
Analyse Crystal structure of engineered anti-ee scfv antibody fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NKD
- Type
- protein
- Length
- 944 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engineered scfv heavy chain; Engineered scfv light chain
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Engineered scfv heavy chain | protein | 121 | 5% helix, 53% strand | — |
| B, D, F, H | Engineered scfv light chain | protein | 115 | 3% helix, 39% strand | — |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.73 | 0.78 | 81 | empty |
| 2 | 295 | 0.55 | 0.76 | 34 | empty |
| 3 | 173 | 0.51 | 0.78 | 19 | empty |
| 4 | 155 | 0.49 | 0.78 | 19 | empty |
| 5 | 119 | 0.47 | 0.79 | 20 | empty |
Interfaces
10 interfaces between chains.
- E–F · 864 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 861 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 858 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 857 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 451 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4NKD · Crystal structure of engineered anti-EE scFv antibody fragment · 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 4NKD · PDBe 4NKD
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