Research workbench
Crystal structure of pcdn-27B, an antibody from the pcdn family of HIV-1 antibodies
Analyse Crystal structure of pcdn-27B, an antibody from the pcdn family of HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BZW
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2B3 HIV antibody light chain; 2B3 HIV antibody heavy chain
- Ligands
- NAG, SO4
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2B3 HIV antibody light chain | protein | 213 | 6% helix, 54% strand | — |
| B | 2B3 HIV antibody heavy chain | protein | 230 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.60 | 0.74 | 66 | empty |
| 2 | 226 | 0.53 | 0.77 | 32 | empty |
| 3 | 73 | 0.33 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1683 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5BZW · Crystal Structure of PCDN-27B, an antibody from the PCDN family of HIV-1 antibodies · 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 5BZW · PDBe 5BZW
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.