Research workbench
Alpha-crystallin domain of human HSPB6 patched with its N-terminal peptide
Analyse Alpha-crystallin domain of human HSPB6 patched with its N-terminal peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LUM
- Type
- protein
- Length
- 435 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein beta-6
- UniProt
- O14558
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, G, H, I, J | Heat shock protein beta-6 | protein | 9 | 0% helix, 67% strand | O14558 |
| A, B, C, D, E | Heat shock protein beta-6 | protein | 78 | 8% helix, 59% strand | O14558 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.62 | 0.79 | 27 | SO4 |
| 2 | 232 | 0.53 | 0.77 | 22 | empty |
| 3 | 199 | 0.53 | 0.78 | 34 | empty |
| 4 | 182 | 0.52 | 0.78 | 25 | empty |
Interfaces
15 interfaces between chains.
- B–C · 971 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 714 Ų buried · 20 hydrogen bonds · protein-protein
- J–E · 518 Ų buried · 10 hydrogen bonds · protein-protein
- F–A · 518 Ų buried · 10 hydrogen bonds · protein-protein
- I–D · 485 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5LUM · Alpha-crystallin domain of human HSPB6 patched with its N-terminal peptide · the same entry in another collection · chain E against E, TM-score 1.00
- O14558 · AlphaFold monomer V2.0 prediction for heat shock protein beta-6 (O14558) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O14558
- Elsewhere: RCSB PDB 5LUM · PDBe 5LUM · UniProt O14558
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