Research workbench
Crystal structure of a highly fibrillogenic ARG24GLY mutant of the recombinant variable domain 6AJL2
Analyse Crystal structure of a highly fibrillogenic ARG24GLY mutant of the recombinant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C9K
- Type
- protein
- Length
- 887 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid lambda 6 light chain variable region pip
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H | Amyloid lambda 6 light chain variable region pip | protein | 111 | 8% helix, 49% strand | — |
| F | Amyloid lambda 6 light chain variable region pip | protein | 110 | 5% helix, 48% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains B, C, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.80 | 0.81 | 98 | empty |
| 2 | 1060 | 0.79 | 0.81 | 86 | empty |
| 3 | 621 | 0.71 | 0.79 | 63 | ACT |
| 4 | 504 | 0.65 | 0.77 | 59 | empty |
| 5 | 367 | 0.56 | 0.75 | 60 | empty |
Interfaces
13 interfaces between chains.
- C–E · 699 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 674 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 663 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 437 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5C9K · Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable… · 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 5C9K · PDBe 5C9K
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