Research workbench
Crystal structure of LI33 IGG2 di-Fab
Analyse Crystal structure of LI33 IGG2 di-Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KYM
- Type
- protein
- Length
- 3,449 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain LI33 IGG2; Heavy chain LI33 IGG2
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, O | Light chain LI33 IGG2 | protein | 213 | 6% helix, 50% strand | — |
| B, D | Heavy chain LI33 IGG2 | protein | 220 | 6% helix, 47% strand | — |
| F, H, J, L, N, P | Heavy chain LI33 IGG2 | protein | 219 | 7% helix, 52% strand | — |
| K | Light chain LI33 IGG2 | protein | 209 | 3% helix, 36% strand | — |
| M | Light chain LI33 IGG2 | protein | 208 | 2% helix, 45% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.87 | 0.88 | 110 | empty |
| 2 | 113 | 0.75 | 0.95 | 31 | empty |
| 3 | 1094 | 0.75 | 0.78 | 126 | empty |
| 4 | 727 | 0.72 | 0.78 | 88 | empty |
| 5 | 221 | 0.64 | 0.82 | 31 | empty |
Interfaces
31 interfaces between chains.
- O–P · 1849 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1825 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1811 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1789 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1775 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 3KYM · Crystal structure of Li33 IgG2 di-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 3KYM · PDBe 3KYM
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