Research workbench
Structure of the G6 Fab, a phage derived VEGF binding Fab
Analyse Structure of the G6 Fab, a phage derived VEGF binding Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FJF
- Type
- protein
- Length
- 5,148 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of a VEGF binding antibody; Heavy chain of a VEGF binding antibody
- UniProt
- Q6GMX8, Q569F4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, C, E, G, J, M, O, Q, S, U, W | Light chain of a VEGF binding antibody | protein | 211 | 6% helix, 50% strand | Q6GMX8 |
| H, B, D, F, I, K, N, P, R, T, V, X | Heavy chain of a VEGF binding antibody | protein | 218 | 8% helix, 50% strand | Q569F4 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.71 | 0.76 | 114 | empty |
| 2 | 1191 | 0.69 | 0.74 | 130 | empty |
| 3 | 704 | 0.68 | 0.76 | 97 | empty |
| 4 | 708 | 0.65 | 0.74 | 92 | empty |
| 5 | 350 | 0.61 | 0.78 | 71 | empty |
Interfaces
56 interfaces between chains.
- W–X · 1897 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1885 Ų buried · 15 hydrogen bonds · protein-protein
- M–N · 1869 Ų buried · 16 hydrogen bonds · protein-protein
- S–T · 1860 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1840 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 2FJF · Structure of the G6 Fab, a phage derived VEGF binding Fab · 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
- Every structure of UniProt Q6GMX8
- Every structure of UniProt Q569F4
- Elsewhere: RCSB PDB 2FJF · PDBe 2FJF · UniProt Q6GMX8 · UniProt Q569F4
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