Research workbench
Crystal structure of human H-chain ferritin variant infused with sodium acrylate
Analyse Crystal structure of human H-chain ferritin variant infused with sodium acrylate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K26
- Type
- protein
- Length
- 2,084 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- FE, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Ferritin heavy chain (EC 1.16.3.1) | protein | 174 | 72% helix, 1% strand | P02794 |
| B, F, H, I, J, L | Ferritin heavy chain (EC 1.16.3.1) | protein | 173 | 72% helix, 0% strand | P02794 |
| D | Ferritin heavy chain (EC 1.16.3.1) | protein | 176 | 71% helix, 1% strand | P02794 |
| E | Ferritin heavy chain (EC 1.16.3.1) | protein | 173 | 72% helix, 1% strand | P02794 |
| K | Ferritin heavy chain (EC 1.16.3.1) | protein | 175 | 71% helix, 0% strand | P02794 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 7 copies · chains A, C, G, E, F, L, B, D, H, J, K
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains B, A, D, C, E, F, H, G, J, K, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.81 | 0.98 | 19 | MPD |
| 2 | 108 | 0.80 | 0.99 | 18 | MPD |
| 3 | 96 | 0.79 | 0.98 | 16 | MPD |
| 4 | 90 | 0.78 | 0.98 | 16 | MPD |
| 5 | 62 | 0.74 | 0.98 | 13 | MPD |
Interfaces
26 interfaces between chains.
- C–E · 1625 Ų buried · 35 hydrogen bonds · protein-protein
- F–H · 1564 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1541 Ų buried · 29 hydrogen bonds · protein-protein
- G–J · 1522 Ų buried · 30 hydrogen bonds · protein-protein
- I–L · 1507 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7K26 · Crystal structure of Human H-chain Ferritin variant infused with Sodium Acrylate · the same entry in another collection · chain L against L, 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 P02794
- Elsewhere: RCSB PDB 7K26 · PDBe 7K26 · UniProt P02794
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