Research workbench
Ki O18/O8 Y87H immunoglobulin light chain variable domain
Analyse Ki O18/O8 Y87H immunoglobulin light chain variable domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CDF
- Type
- protein
- Length
- 651 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immuglobulin light chain
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Immuglobulin light chain | protein | 108 | 3% helix, 48% strand | — |
| B, D, F | Immuglobulin light chain | protein | 109 | 3% helix, 47% strand | — |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.76 | 0.81 | 84 | empty |
| 2 | 117 | 0.44 | 0.77 | 24 | empty |
| 3 | 132 | 0.43 | 0.77 | 26 | empty |
| 4 | 147 | 0.43 | 0.75 | 28 | empty |
| 5 | 95 | 0.36 | 0.75 | 20 | empty |
Interfaces
10 interfaces between chains.
- E–F · 747 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 746 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 701 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 687 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 272 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3CDF · kI O18/O8 Y87H immunoglobulin light chain variable domain · 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 3CDF · PDBe 3CDF
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