Research workbench
Broadly neutralizing darpin BND.3 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-if (BG505)
Analyse Broadly neutralizing darpin BND.3 in complex with the HIV-1 envelope variable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B4W
- Type
- protein
- Length
- 350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Broadly neutralizing darpin BND.3; HIV-1 envelope variable loop 3 crown mimetic peptide…
- Ligands
- CA, NA
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Broadly neutralizing darpin BND.3 | protein | 161 | 57% helix, 0% strand | — |
| C | Broadly neutralizing darpin BND.3 | protein | 159 | 54% helix, 0% strand | — |
| B, D | HIV-1 envelope variable loop 3 crown mimetic peptide V3-if (BG505) | protein | 15 | 0% helix, 13% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.69 | 0.78 | 71 | empty |
| 2 | 51 | 0.27 | 0.74 | 13 | empty |
Interfaces
4 interfaces between chains.
- C–D · 726 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 696 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 d-amino (D-amino acid).
Compared structures
- 7B4W · Broadly neutralizing DARPin bnD.3 in complex with the HIV-1 envelope variable loop 3… · 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 7B4W · PDBe 7B4W
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