Research workbench
Crystal structure of germline antibody PGT121-gl Fab
Analyse Crystal structure of germline antibody PGT121-gl Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FQQ
- Type
- protein
- Length
- 1,752 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Ligands
- NA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 8 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 213 | 8% helix, 47% strand | — |
| H | Fab heavy chain | protein | 234 | 8% helix, 54% strand | — |
| A | Fab light chain | protein | 211 | 6% helix, 47% strand | — |
| B | Fab heavy chain | protein | 227 | 4% helix, 53% strand | — |
| C | Fab light chain | protein | 210 | 8% helix, 48% strand | — |
| D | Fab heavy chain | protein | 226 | 4% helix, 54% strand | — |
| E | Fab light chain | protein | 205 | 5% helix, 48% strand | — |
| F | Fab heavy chain | protein | 226 | 7% helix, 56% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains L, H, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.69 | 0.78 | 61 | empty |
| 2 | 336 | 0.53 | 0.74 | 50 | empty |
| 3 | 289 | 0.50 | 0.73 | 51 | empty |
| 4 | 82 | 0.49 | 0.83 | 16 | empty |
| 5 | 271 | 0.48 | 0.73 | 42 | empty |
Interfaces
12 interfaces between chains.
- L–H · 1965 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1825 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1815 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1808 Ų buried · 18 hydrogen bonds · protein-protein
- H–A · 445 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4FQQ · Crystal Structure of Germline Antibody PGT121-GL Fab · the same entry in another collection · chain L against L, 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 4FQQ · PDBe 4FQQ
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