Research workbench
Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in complex with GP41 peptide LELDKWASLW[N-ac]
Analyse Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P8P
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nmab 2F5, light chain; Nmab 2F5, heavy chain; GP41 peptide
- Ligands
- NH2
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nmab 2F5, light chain | protein | 214 | 5% helix, 49% strand | — |
| B | Nmab 2F5, heavy chain | protein | 221 | 4% helix, 52% strand | — |
| C | GP41 peptide | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 345 | 0.55 | 0.75 | 49 | empty |
| 2 | 76 | 0.31 | 0.74 | 16 | empty |
| 3 | 69 | 0.30 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1877 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2P8P · Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with… · 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 2P8P · PDBe 2P8P
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