MolNFT v1 · #36426 · protein
Crystal structure of Fab' from the HIV-1 neutralizing antibody 2F5 in complex with its GP41 epitope
2F5B · Protein (antibody 2F5 (light chain)): “Crystal structure of Fab' from the HIV-1 neutralizing antibody 2F5 in complex with its GP41 epitope”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #36426 on GenesisL1: 3D…
- PDB
- 2F5B
- Type
- protein
- Length
- 452 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (antibody 2F5 (light chain)); Protein (antibody 2F5 (heavy chain)); Protein (GP41…
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (antibody 2F5 (light chain)) | protein | 214 | 6% helix, 50% strand | — |
| H | Protein (antibody 2F5 (heavy chain)) | protein | 231 | 9% helix, 50% strand | — |
| P | Protein (GP41 epitope) | protein | 7 | 0% helix, 14% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.58 | 0.74 | 54 | empty |
| 2 | 155 | 0.41 | 0.73 | 31 | empty |
| 3 | 58 | 0.26 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1819 Ų buried · 16 hydrogen bonds · protein-protein
- H–P · 355 Ų buried · 8 hydrogen bonds · protein-protein
- L–P · 247 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2F5B · Crystal structure of Fab' from the HIV-1 neutralizing antibody 2F5 in complex with its… · 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
- Elsewhere: RCSB PDB 2F5B · PDBe 2F5B
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