Research workbench
Mouse antibody 3.3 Fab in complex with peg
Analyse Mouse antibody 3.3 Fab in complex with peg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JU0
- Type
- protein
- Length
- 1,702 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain
- Ligands
- TOE
- Pockets
- 17 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | Fab heavy chain | protein | 212 | 8% helix, 55% strand | — |
| L, M, N, O | Fab light chain | protein | 213 | 8% helix, 51% strand | — |
| I, K | Fab heavy chain | protein | 213 | 8% helix, 54% strand | — |
Ligands and binding sites
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · 4 copies · chains H, L, I, M, J, N, K, O
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 2 copies · chains H, L, I, M, J, N, K, O
- 1PE · Pentaethylene glycol · additive · chains H
- PG4 · Tetraethylene glycol · additive · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.67 | 0.79 | 50 | empty |
| 2 | 743 | 0.66 | 0.75 | 73 | empty |
| 3 | 436 | 0.65 | 0.78 | 44 | empty |
| 4 | 669 | 0.65 | 0.75 | 62 | empty |
| 5 | 720 | 0.65 | 0.74 | 75 | empty |
Interfaces
14 interfaces between chains.
- H–L · 1792 Ų buried · 17 hydrogen bonds · protein-protein
- K–O · 1789 Ų buried · 15 hydrogen bonds · protein-protein
- J–N · 1781 Ų buried · 15 hydrogen bonds · protein-protein
- I–M · 1760 Ų buried · 16 hydrogen bonds · protein-protein
- I–K · 411 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 modified (disulfide, cyclization).
Compared structures
- 6JU0 · Mouse antibody 3.3 Fab in complex with PEG · the same entry in another collection · chain H against H, 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 6JU0 · PDBe 6JU0
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