Research workbench
Crystal structure of the amyloid-forming immunoglobulin al-103 cis- proline 95 mutant
Analyse Crystal structure of the amyloid-forming immunoglobulin al-103 cis- proline 95… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K07
- Type
- protein
- Length
- 1,080 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloidogenic immunoglobulin light chain protein al-103
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Amyloidogenic immunoglobulin light chain protein al-103 | protein | 108 | 3% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.77 | 0.79 | 108 | empty |
| 2 | 331 | 0.53 | 0.74 | 37 | empty |
| 3 | 120 | 0.42 | 0.76 | 22 | empty |
| 4 | 91 | 0.40 | 0.77 | 17 | empty |
| 5 | 123 | 0.40 | 0.75 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–B · 732 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 730 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 719 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 713 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 713 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4K07 · Crystal structure of the amyloid-forming immunoglobulin AL-103 cis-proline 95 mutant · 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 4K07 · PDBe 4K07
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