MolNFT v1 · #61651 · protein
Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the GP41 scrambledfp-mper SCRHYB3K construct gigafgllgflaagskk-ahx-K656NEQELLELDKWASLWN671
3DRT · 2F5 Fab' light chain: “Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the GP41 scrambledfp-mper…”. X-ray diffraction, 4 pockets (best druggability 0.56). MolNFT v1 #61651 on GenesisL1: 3D structure…
- PDB
- 3DRT
- Type
- protein
- Length
- 435 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2F5 Fab' light chain; 2F5 Fab' heavy chain; SCRHYB3K construct
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2F5 Fab' light chain | protein | 213 | 3% helix, 52% strand | — |
| B | 2F5 Fab' heavy chain | protein | 216 | 8% helix, 50% strand | — |
| C | SCRHYB3K construct | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.56 | 0.75 | 45 | empty |
| 2 | 52 | 0.46 | 0.86 | 22 | GOL |
| 3 | 64 | 0.30 | 0.74 | 13 | empty |
| 4 | 78 | 0.28 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1808 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 299 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3DRT · Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41… · 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 3DRT · PDBe 3DRT
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