Research workbench
Structure of monomeric mutant of rei immunoglobulin light chain variable domain crystallized at pH 6
Analyse Structure of monomeric mutant of rei 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
- 5XP1
- Type
- protein
- Length
- 870 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin kappa variable 1D-33
- UniProt
- P01593
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Immunoglobulin kappa variable 1D-33 | protein | 109 | 3% helix, 50% strand | P01593 |
| G | Immunoglobulin kappa variable 1D-33 | protein | 107 | 3% helix, 41% strand | P01593 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.73 | 0.78 | 65 | empty |
| 2 | 130 | 0.52 | 0.81 | 28 | empty |
| 3 | 98 | 0.48 | 0.81 | 20 | empty |
Interfaces
8 interfaces between chains.
- D–E · 456 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 442 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 441 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 439 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 317 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5XP1 · Structure of monomeric mutant of REI immunoglobulin light chain variable domain… · the same entry in another collection · chain H against H, TM-score 1.00
- P01593 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa variable 1D-33 (P01593) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P01593
- Elsewhere: RCSB PDB 5XP1 · PDBe 5XP1 · UniProt P01593
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