MolNFT v1 · #121878 · protein
Crystal structure of HIV-1 clade a BG505 fusion peptide (residue 512- 520) in complex with broadly neutralizing antibody VRC34.01 Fab
5I8C · VRC34.01 Fab heavy chain: “Crystal structure of HIV-1 clade a BG505 fusion peptide (residue 512- 520) in complex with broadly…”. X-ray diffraction, 5 pockets (best druggability 0.61). MolNFT v1 #121878 on GenesisL1: 3D structure…
- PDB
- 5I8C
- Type
- protein
- Length
- 443 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC34.01 Fab heavy chain; VRC34.01 Fab light chain; HIV-1 clade a BG505 fusion peptide…
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VRC34.01 Fab heavy chain | protein | 223 | 9% helix, 50% strand | — |
| B | VRC34.01 Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| C | HIV-1 clade a BG505 fusion peptide (residue 512-520) | protein | 8 | 0% helix, 0% strand | — |
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 | 458 | 0.61 | 0.76 | 49 | empty |
| 2 | 69 | 0.51 | 0.86 | 22 | empty |
| 3 | 202 | 0.49 | 0.75 | 34 | empty |
| 4 | 61 | 0.29 | 0.74 | 22 | empty |
| 5 | 64 | 0.27 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1785 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 178 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5I8C · Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) 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 5I8C · PDBe 5I8C
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