Research workbench
The unliganded germline precursor to the sulfide oxidase catalytic antibody 28B4.
Analyse The unliganded germline precursor to the sulfide oxidase catalytic antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FL5
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody germline precursor to antibody 28B4
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Antibody germline precursor to antibody 28B4 | protein | 217 | 6% helix, 53% strand | — |
| H, B | Antibody germline precursor to antibody 28B4 | protein | 219 | 7% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains L, H, A, B
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 | 611 | 0.70 | 0.79 | 64 | empty |
| 2 | 242 | 0.57 | 0.79 | 31 | empty |
| 3 | 331 | 0.55 | 0.75 | 41 | empty |
| 4 | 95 | 0.53 | 0.84 | 19 | empty |
| 5 | 97 | 0.53 | 0.83 | 20 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1948 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1945 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 781 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 121 Ų buried · 1 hydrogen bond · protein-protein
- L–B · 75 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1FL5 · The unliganded germline precursor to the sulfide oxidase catalytic antibody 28B4. · 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 1FL5 · PDBe 1FL5
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