Research workbench
Structure of IGLB12 Fab in complex with anti-idiotype IB3 Fab
Analyse Structure of IGLB12 Fab in complex with anti-idiotype IB3 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OL5
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IB3 heavy chain; IB3 light chain; IGLB12 heavy chain; IGLB12 light chain
- Ligands
- NH4, PO4, CL
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IB3 heavy chain | protein | 210 | 9% helix, 54% strand | — |
| B | IB3 light chain | protein | 213 | 6% helix, 53% strand | — |
| H | IGLB12 heavy chain | protein | 228 | 7% helix, 50% strand | — |
| L | IGLB12 light chain | protein | 212 | 7% helix, 53% strand | — |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 18 copies · chains A, B, H, L
- PO4 · Phosphate ion · ion · 14 copies · chains A, B, H, L
- CL · Chloride ion · ion · 13 copies · chains A, B, H, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.66 | 0.74 | 75 | NH4, PO4 |
| 2 | 55 | 0.61 | 0.92 | 19 | PO4 |
| 3 | 436 | 0.59 | 0.75 | 51 | empty |
| 4 | 124 | 0.57 | 0.84 | 25 | CL, PO4 |
| 5 | 106 | 0.49 | 0.81 | 27 | NH4, PO4, CL |
Interfaces
6 interfaces between chains.
- H–L · 2058 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 653 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 380 Ų buried · 4 hydrogen bonds · protein-protein
- B–L · 307 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 6OL5 · Structure of iglb12 Fab in complex with anti-idiotype ib3 Fab · 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 6OL5 · PDBe 6OL5
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