MolNFT v1 · #186425 · protein
Crystal structure of pcdn-16B, an anti-HIV antibody from the pcdn bnab lineage (non-cysteinylated state)
7RDJ · Pcdn-16B Fab light chain: “Crystal structure of pcdn-16B, an anti-HIV antibody from the pcdn bnab lineage (non-cysteinylated state)”. X-ray diffraction, 5 pockets (best druggability 0.54). MolNFT v1 #186425 on GenesisL1: 3D…
- PDB
- 7RDJ
- Type
- protein
- Length
- 440 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
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pcdn-16B Fab light chain | protein | 215 | 6% helix, 53% strand | — |
| B | Pcdn-16B Fab heavy chain | protein | 225 | 9% helix, 52% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.54 | 0.77 | 36 | empty |
| 2 | 256 | 0.48 | 0.73 | 38 | EDO |
| 3 | 50 | 0.29 | 0.76 | 11 | EDO |
| 4 | 55 | 0.26 | 0.73 | 15 | EDO |
| 5 | 55 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1679 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RDJ · Crystal structure of PCDN-16B, 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 7RDJ · PDBe 7RDJ
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