Research workbench
Crystal structure of pcdn-16B, an anti-HIV antibody from the pcdn bnab lineage (cysteinylated state)
Analyse Crystal structure of pcdn-16B, an anti-HIV antibody from the pcdn bnab lineage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RDK
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pcdn-16B Fab light chain; Pcdn-16B Fab heavy chain
- Ligands
- CYS, SO4
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pcdn-16B Fab light chain | protein | 215 | 6% helix, 51% strand | — |
| B | Pcdn-16B Fab heavy chain | protein | 229 | 3% helix, 52% strand | — |
Ligands and binding sites
- CYS · Cysteine · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
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 | 376 | 0.56 | 0.74 | 48 | empty |
| 2 | 69 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1932 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7RDK · Crystal structure of PCDN-16B, an anti-HIV antibody from the PCDN bnAb lineage… · the same entry in another collection · chain B against B, 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 7RDK · PDBe 7RDK
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