Research workbench
Crystal structure of pcdn-22A, an anti-HIV antibody from the pcdn bnab lineage
Analyse Crystal structure of pcdn-22A, 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
- 7RDL
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pcdn-22A Fab light chain; Pcdn-22A Fab heavy chain
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pcdn-22A Fab light chain | protein | 215 | 6% helix, 53% strand | — |
| B | Pcdn-22A Fab heavy chain | protein | 217 | 4% helix, 52% strand | — |
| D | Pcdn-22A Fab heavy chain | protein | 223 | 4% helix, 52% strand | — |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.68 | 0.83 | 29 | empty |
| 2 | 63 | 0.60 | 0.91 | 21 | empty |
| 3 | 364 | 0.60 | 0.77 | 34 | empty |
| 4 | 299 | 0.59 | 0.78 | 36 | empty |
| 5 | 373 | 0.56 | 0.75 | 50 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1785 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1649 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 637 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7RDL · Crystal structure of PCDN-22A, an anti-HIV antibody from the PCDN bnAb lineage · 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 7RDL · PDBe 7RDL
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