Research workbench
Crystal structure of engineered antibody fragment based on 3D5
Analyse Crystal structure of engineered antibody fragment based on 3D5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NN8
- Type
- protein
- Length
- 947 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
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Engineered scfv, heavy chain | protein | 121 | 5% helix, 54% strand | — |
| B, E | Engineered scfv, light chain | protein | 115 | 3% helix, 46% strand | — |
| C | Engineered scfv, heavy chain | protein | 122 | 5% helix, 49% strand | — |
| F, H | Engineered scfv, light chain | protein | 116 | 3% helix, 47% strand | — |
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.73 | 0.80 | 55 | empty |
| 2 | 617 | 0.72 | 0.80 | 54 | empty |
| 3 | 142 | 0.47 | 0.78 | 18 | empty |
| 4 | 97 | 0.42 | 0.78 | 18 | empty |
| 5 | 60 | 0.35 | 0.78 | 18 | empty |
Interfaces
12 interfaces between chains.
- G–H · 902 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 902 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 899 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 899 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 493 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3NN8 · Crystal structure of engineered antibody fragment based on 3D5 · 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 3NN8 · PDBe 3NN8
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