Research workbench
Structure of IGLB12 scfv in complex with anti-idiotype IB2 Fab
Analyse Structure of IGLB12 scfv in complex with anti-idiotype IB2 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OL6
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IB2 heavy chain; IB2 light chain; IGLB12 heavy chain; IGLB12 light chain
- Ligands
- CL
- Pockets
- 11 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IB2 heavy chain | protein | 216 | 9% helix, 54% strand | — |
| B | IB2 light chain | protein | 212 | 5% helix, 51% strand | — |
| H | IGLB12 heavy chain | protein | 127 | 10% helix, 46% strand | — |
| L | IGLB12 light chain | protein | 113 | 5% helix, 54% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.46 | 0.75 | 33 | empty |
| 2 | 197 | 0.46 | 0.74 | 25 | CL |
| 3 | 126 | 0.42 | 0.76 | 24 | empty |
| 4 | 66 | 0.33 | 0.76 | 16 | empty |
| 5 | 76 | 0.33 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1741 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 945 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 495 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 259 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6OL6 · Structure of iglb12 scFv in complex with anti-idiotype ib2 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 6OL6 · PDBe 6OL6
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