MolNFT v1 · #175400 · protein
His-mediated reversible self-assembly of ferritin nanocage with zn binding
7CPI: “His-mediated reversible self-assembly of ferritin nanocage with zn binding”. X-ray diffraction, 2 ligands (FE, ZN), 13 pockets (best druggability 0.78). MolNFT v1 #175400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CPI
- Type
- protein
- Length
- 1,002 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
- FE, ZN
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, B, C, D, F | Ferritin (EC 1.16.3.1) | protein | 167 | 74% helix, 0% strand | T2B7E1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains E, A, B, C, D, F
- ZN · Zinc ion · metal · 7 copies · chains A, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.78 | 0.96 | 20 | empty |
| 2 | 784 | 0.77 | 0.81 | 65 | empty |
| 3 | 93 | 0.76 | 0.97 | 18 | empty |
| 4 | 735 | 0.70 | 0.77 | 51 | empty |
| 5 | 176 | 0.61 | 0.83 | 39 | empty |
Interfaces
9 interfaces between chains.
- A–F · 1517 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1480 Ų buried · 29 hydrogen bonds · protein-protein
- E–D · 727 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 723 Ų buried · 8 hydrogen bonds · protein-protein
- E–C · 589 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7CPI · His-Mediated Reversible Self-assembly of Ferritin Nanocage with Zn binding · the same entry in another collection · chain E against E, 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 7CPI · PDBe 7CPI · UniProt T2B7E1
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