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The first crystal structure of crustacean ferritin that is a hybrid type of H and L ferritin
Analyse The first crystal structure of crustacean ferritin that is a hybrid type of H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A4U
- Type
- protein
- Length
- 1,014 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- T2B7E1
- Ligands
- MG, SO4, CL
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ferritin (EC 1.16.3.1) | protein | 169 | 74% helix, 1% strand | T2B7E1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains C, D, F
- SO4 · Sulfate ion · ion · 13 copies · chains A, C, D, B, E, F
- CL · Chloride ion · ion · chains B, E
- EDO · 1,2-ethanediol · additive · 50 copies · chains A, D, F, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.80 | 0.87 | 75 | EDO |
| 2 | 1007 | 0.79 | 0.80 | 75 | SO4 |
| 3 | 91 | 0.78 | 0.98 | 15 | SO4 |
| 4 | 87 | 0.76 | 0.97 | 17 | SO4 |
| 5 | 89 | 0.75 | 0.97 | 16 | SO4 |
Interfaces
9 interfaces between chains.
- A–D · 1402 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1394 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 1378 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 734 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 564 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6A4U · The first crystal structure of crustacean ferritin that is a hybrid type of H and L… · 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
- Every structure of UniProt T2B7E1
- Elsewhere: RCSB PDB 6A4U · PDBe 6A4U · UniProt T2B7E1
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