MolNFT v1 · #71782 · protein
Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced IgG) with 11 aa GP41 mper-derived peptide
3MOD: “Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced IgG) with 11 aa…”. X-ray diffraction, 1 ligand (NH2), 4 pockets (best druggability 0.53). MolNFT v1 #71782 on GenesisL1: 3D structure…
- PDB
- 3MOD
- Type
- protein
- Length
- 462 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP41 mper-derived peptide; Anti-HIV-1 antibody 2F5 light chain; Anti-HIV-1 antibody 2F5…
- Ligands
- NH2
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | GP41 mper-derived peptide | protein | 11 | 0% helix, 18% strand | — |
| L | Anti-HIV-1 antibody 2F5 light chain | protein | 214 | 6% helix, 51% strand | — |
| H | Anti-HIV-1 antibody 2F5 heavy chain | protein | 237 | 9% helix, 49% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · chains P, H
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 | 329 | 0.53 | 0.74 | 41 | empty |
| 2 | 109 | 0.40 | 0.76 | 19 | empty |
| 3 | 55 | 0.29 | 0.75 | 15 | empty |
| 4 | 56 | 0.24 | 0.71 | 11 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2004 Ų buried · 18 hydrogen bonds · protein-protein
- P–H · 456 Ų buried · 10 hydrogen bonds · protein-protein
- P–L · 332 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3MOD · Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly… · the same entry in another collection · chain P against P, 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 3MOD · PDBe 3MOD
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