MolNFT v1 · #22890 · protein
Crystal structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a GP41 17MER epitope
1TJI · Anti-HIV-1 antibody 2F5 light chain: “Crystal structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a GP41 17MER epitope”. X-ray diffraction, 1 ligand (NH2), 5 pockets (best druggability 0.54). MolNFT v1…
- PDB
- 1TJI
- Type
- protein
- Length
- 465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HIV-1 antibody 2F5 light chain; Anti-HIV-1 antibody 2F5 heavy chain; Envelope…
- UniProt
- P04580
- Ligands
- NH2
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-HIV-1 antibody 2F5 light chain | protein | 214 | 7% helix, 51% strand | — |
| H | Anti-HIV-1 antibody 2F5 heavy chain | protein | 237 | 9% helix, 50% strand | — |
| P | Envelope glycoprotein GP41 | protein | 14 | 0% helix, 14% strand | P04580 |
Ligands and binding sites
- NH2 · Amino group · ion · chains H, P
- IPA · Isopropyl alcohol · additive · 6 copies · chains L, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains L, H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.54 | 0.74 | 49 | IPA |
| 2 | 162 | 0.51 | 0.79 | 21 | empty |
| 3 | 60 | 0.49 | 0.86 | 21 | empty |
| 4 | 58 | 0.30 | 0.76 | 16 | empty |
| 5 | 57 | 0.28 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2081 Ų buried · 18 hydrogen bonds · protein-protein
- H–P · 459 Ų buried · 10 hydrogen bonds · protein-protein
- L–P · 419 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, alkylation).
Compared structures
- 1TJI · Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a… · 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
- Every structure of UniProt P04580
- Elsewhere: RCSB PDB 1TJI · PDBe 1TJI · UniProt P04580
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