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Crystal structure of human ferritin H8 as biotemplate for noble metal nanoparticle synthesis
Analyse Crystal structure of human ferritin H8 as biotemplate for noble metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z6M
- 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
- ZN, CA
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 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 | Ferritin heavy chain (EC 1.16.3.1) | protein | 172 | 72% helix, 1% strand | P02794 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, D, B, G, J, H, I
- CA · Calcium ion · metal · 4 copies · chains A, C, E, B, D, F, G, I, K, H, J, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains B, C, E, A, F, H, I, G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.86 | 0.87 | 112 | empty |
| 2 | 92 | 0.79 | 0.99 | 17 | MPD |
| 3 | 99 | 0.79 | 0.98 | 17 | MPD |
| 4 | 520 | 0.72 | 0.81 | 60 | empty |
| 5 | 277 | 0.68 | 0.84 | 36 | empty |
Interfaces
21 interfaces between chains.
- G–L · 1548 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 1538 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 730 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 730 Ų buried · 9 hydrogen bonds · protein-protein
- G–K · 727 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2Z6M · Crystal structure of Human Ferritin H8 as biotemplate for noble metal nanoparticle… · 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 2Z6M · PDBe 2Z6M · UniProt P02794
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