Research workbench
Crystal structure of pcdn-38B, a broadly neutralizing anti-HIV antibody
Analyse Crystal structure of pcdn-38B, a broadly neutralizing anti-HIV antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RDM
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pcdn-38B Fab light chain; Pcdn-38B Fab heavy chain
- Ligands
- CYS, NAG, BMA, MAN, FUC, PO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pcdn-38B Fab light chain | protein | 216 | 6% helix, 53% strand | — |
| B | Pcdn-38B Fab heavy chain | protein | 231 | 7% helix, 53% strand | — |
Ligands and binding sites
- CYS · Cysteine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.61 | 0.74 | 62 | PO4 |
| 2 | 237 | 0.55 | 0.77 | 36 | GOL |
| 3 | 62 | 0.44 | 0.82 | 13 | CYS |
| 4 | 87 | 0.33 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1821 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 7RDM · Crystal structure of PCDN-38B, a broadly neutralizing anti-HIV 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 7RDM · PDBe 7RDM
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