MolNFT v1 · #47775 · protein
Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in complex with GP41 peptide elleldkwaslwn in new crystal form
2P8M · Nmab 2F5, light chain: “Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in complex with GP41 peptide…”. X-ray diffraction, 4 pockets (best druggability 0.58). MolNFT v1 #47775 on GenesisL1: 3D structure…
- PDB
- 2P8M
- Type
- protein
- Length
- 439 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
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nmab 2F5, light chain | protein | 213 | 7% helix, 51% strand | — |
| B | Nmab 2F5, heavy chain | protein | 217 | 6% helix, 51% strand | — |
| C | GP41 peptide | protein | 9 | 0% helix, 22% strand | — |
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 | 398 | 0.58 | 0.75 | 49 | empty |
| 2 | 73 | 0.30 | 0.73 | 14 | empty |
| 3 | 77 | 0.30 | 0.73 | 15 | empty |
| 4 | 57 | 0.24 | 0.72 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1854 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2P8M · 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 2P8M · PDBe 2P8M
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