Research workbench
Crystal structure of broadly neutralizing HIV-1 fusion peptide- targeting antibody VRC34.01 Fab
Analyse Crystal structure of broadly neutralizing HIV-1 fusion peptide- targeting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I8E
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC34.01 Fab heavy chain; VRC34.01 Fab light chain
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VRC34.01 Fab heavy chain | protein | 217 | 8% helix, 49% strand | — |
| B | VRC34.01 Fab light chain | protein | 203 | 3% helix, 47% strand | — |
| C | VRC34.01 Fab heavy chain | protein | 216 | 10% helix, 50% strand | — |
| D | VRC34.01 Fab light chain | protein | 210 | 6% helix, 49% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.59 | 0.75 | 53 | empty |
| 2 | 383 | 0.55 | 0.74 | 53 | empty |
| 3 | 124 | 0.53 | 0.82 | 22 | empty |
| 4 | 62 | 0.29 | 0.74 | 16 | empty |
| 5 | 50 | 0.27 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1796 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1781 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 88 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5I8E · Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeting Antibody… · 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 5I8E · PDBe 5I8E
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