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
- 4NKO
- Type
- protein
- Length
- 708 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engineered scfv light chain; Engineered scfv heavy chain
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Engineered scfv light chain | protein | 115 | 3% helix, 46% strand | — |
| B, D, F | Engineered scfv heavy chain | protein | 121 | 2% helix, 47% strand | — |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.70 | 0.87 | 33 | empty |
| 2 | 59 | 0.69 | 0.96 | 20 | empty |
| 3 | 684 | 0.69 | 0.77 | 65 | empty |
| 4 | 200 | 0.69 | 0.86 | 36 | empty |
| 5 | 120 | 0.51 | 0.81 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 815 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 805 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 802 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 369 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 367 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4NKO · 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 4NKO · PDBe 4NKO
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