Research workbench
Cryo-EM structure of human apoferritin light chain vitrified using back-it-up
Analyse Cryo-EM structure of human apoferritin light chain vitrified using back-it-up in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WX6
- Type
- protein
- Length
- 4,128 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin light chain
- UniProt
- P02792
- Ligands
- CA
- Pockets
- 20 · best druggability 0.70
Structure
electron microscopy · 1 distinct chain · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Ferritin light chain | protein | 172 | 72% helix, 1% strand | P02792 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, F, L, B, H, I, C, G, K, D, E, J, M, R, X, N, T, U, O, S, W, P, Q, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.70 | 0.91 | 29 | empty |
| 2 | 117 | 0.69 | 0.91 | 29 | empty |
| 3 | 117 | 0.68 | 0.90 | 28 | empty |
| 4 | 112 | 0.68 | 0.91 | 25 | empty |
| 5 | 120 | 0.68 | 0.90 | 30 | empty |
Interfaces
72 interfaces between chains.
- G–S · 1478 Ų buried · 23 hydrogen bonds · protein-protein
- H–R · 1478 Ų buried · 23 hydrogen bonds · protein-protein
- E–Q · 1477 Ų buried · 23 hydrogen bonds · protein-protein
- F–T · 1477 Ų buried · 23 hydrogen bonds · protein-protein
- J–M · 1477 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6WX6 · Cryo-EM Structure of Human Apoferritin Light Chain Vitrified Using Back-it-up · the same entry in another collection · chain K against K, 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 P02792
- Elsewhere: RCSB PDB 6WX6 · PDBe 6WX6 · UniProt P02792
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