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
- 4NKM
- 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
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Engineered scfv heavy chain | protein | 121 | 5% helix, 51% strand | — |
| B, D, F, H | Engineered scfv light chain | protein | 115 | 0% helix, 40% strand | — |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.76 | 0.79 | 89 | empty |
| 2 | 441 | 0.66 | 0.78 | 53 | empty |
| 3 | 135 | 0.49 | 0.79 | 22 | empty |
| 4 | 127 | 0.44 | 0.77 | 21 | empty |
| 5 | 101 | 0.42 | 0.77 | 24 | empty |
Interfaces
13 interfaces between chains.
- C–D · 857 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 853 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 852 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 844 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 391 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4NKM · 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 4NKM · PDBe 4NKM
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.