Research workbench
Crystal structure of the unstable and highly fibrillogenic PRO7SER mutant of the recombinant variable domain 6AJL2
Analyse Crystal structure of the unstable and highly fibrillogenic PRO7SER mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BDX
- Type
- protein
- Length
- 333 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid lambda 6 light chain variable region pip (fragment)
- UniProt
- Q96JD1
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Amyloid lambda 6 light chain variable region pip (fragment) | protein | 111 | 5% helix, 50% strand | Q96JD1 |
Ligands and binding sites
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.67 | 0.75 | 86 | ACT, GOL, MES |
| 2 | 58 | 0.28 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 607 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 596 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3BDX · Crystal structure of the unstable and highly fibrillogenic Pro7Ser mutant of the… · 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
- Every structure of UniProt Q96JD1
- Elsewhere: RCSB PDB 3BDX · PDBe 3BDX · UniProt Q96JD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.