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Binary crystal structure of positively and negatively supercharged variants FTN(POS) and FTN(NEG) from human heavy chain ferritin (mg acetate condition)
Analyse Binary crystal structure of positively and negatively supercharged variants… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JKM
- Type
- protein
- Length
- 2,064 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
- MG, FE
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ferritin heavy chain (EC 1.16.3.1) | protein | 172 | 73% helix, 1% strand | P02794 |
| G, H, I, J, K, L | Ferritin heavy chain (EC 1.16.3.1) | protein | 172 | 73% helix, 1% strand | P02794 |
Ligands and binding sites
- MG · Magnesium ion · metal · 17 copies · chains A, C, B, D, E, F, G, I, H, J, L, K
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 2 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.84 | 0.87 | 98 | empty |
| 2 | 85 | 0.78 | 0.99 | 14 | empty |
| 3 | 324 | 0.66 | 0.82 | 38 | MG |
| 4 | 170 | 0.58 | 0.82 | 28 | empty |
| 5 | 240 | 0.54 | 0.77 | 30 | empty |
Interfaces
22 interfaces between chains.
- K–L · 1587 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1574 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1567 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1540 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 724 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5JKM · Binary crystal structure of positively and negatively supercharged variants Ftn(pos) and… · 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 5JKM · PDBe 5JKM · UniProt P02794
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