Research workbench
Structure of the germline VK1 O18/O8 light chain variable domain homodimer
Analyse Structure of the germline VK1 O18/O8 light chain variable domain homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q20
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VK1 O18/O8 germline light chain variable domain
- UniProt
- P01594
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VK1 O18/O8 germline light chain variable domain | protein | 108 | 3% helix, 50% strand | P01594 |
| B | VK1 O18/O8 germline light chain variable domain | protein | 109 | 3% helix, 48% strand | P01594 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.45 | 0.76 | 28 | empty |
| 2 | 128 | 0.41 | 0.75 | 19 | empty |
| 3 | 116 | 0.38 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2Q20 · Structure of the germline Vk1 O18/O8 light chain variable domain homodimer · the same entry in another collection · chain A against A, TM-score 1.00
- P01594 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa variable 1-33 (P01594) · a predicted model of the same protein · chain A against A, TM-score 0.88
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01594
- Elsewhere: RCSB PDB 2Q20 · PDBe 2Q20 · UniProt P01594
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