Research workbench
The hapten complexed germline precursor to sulfide oxidase catalytic antibody 28B4
Analyse The hapten complexed germline precursor to 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
- 1FL6
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody germline precursor to 28B4
- Ligands
- AAH
- Pockets
- 9 · best druggability 0.64
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 28B4 | protein | 217 | 6% helix, 48% strand | — |
| H, B | Antibody germline precursor to 28B4 | protein | 219 | 5% helix, 52% strand | — |
Ligands and binding sites
- AAH · 1-[N-4'-nitrobenzyl-N-4'-carboxybutylamino]methylphosphonic acid · ligand · 2 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.64 | 0.74 | 62 | empty |
| 2 | 634 | 0.63 | 0.74 | 64 | empty |
| 3 | 160 | 0.51 | 0.79 | 31 | empty |
| 4 | 182 | 0.50 | 0.77 | 33 | empty |
| 5 | 100 | 0.42 | 0.78 | 21 | AAH |
Interfaces
2 interfaces between chains.
- L–H · 1760 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1757 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1FL6 · The hapten complexed germline precursor to 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 1FL6 · PDBe 1FL6
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