MolNFT v1 · #139468 · protein
The ferritin E-domain: toward understanding its role in protein cage assembly through the crystal structure of a maxi-/mini-ferritin chimera
5XGO · DNA protection during starvation PROTEIN,BACTERIOFERRITIN: “The ferritin E-domain: toward understanding its role in protein cage assembly through the crystal structure…”. X-ray diffraction, 1 ligand (CL), 20 pockets (best…
- PDB
- 5XGO
- Type
- protein
- Length
- 1,867 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation PROTEIN,BACTERIOFERRITIN
- EC
- 1.16.-.-, 1.16.3.1
- UniProt
- P0ABT2, P0ABD3
- Ligands
- CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, J, L | DNA protection during starvation PROTEIN,BACTERIOFERRITIN (EC 1.16.-.-, 1.16.3.1) | protein | 155 | 74% helix, 1% strand | P0ABT2, P0ABD3 |
| B, D, F, G, H, I, K | DNA protection during starvation PROTEIN,BACTERIOFERRITIN (EC 1.16.-.-, 1.16.3.1) | protein | 156 | 73% helix, 1% strand | P0ABT2, P0ABD3 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.71 | 0.98 | 19 | empty |
| 2 | 50 | 0.68 | 0.97 | 19 | empty |
| 3 | 243 | 0.55 | 0.77 | 17 | empty |
| 4 | 240 | 0.54 | 0.77 | 18 | empty |
| 5 | 235 | 0.54 | 0.77 | 19 | empty |
Interfaces
30 interfaces between chains.
- D–H · 1649 Ų buried · 19 hydrogen bonds · protein-protein
- B–G · 1639 Ų buried · 18 hydrogen bonds · protein-protein
- C–K · 1638 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 1633 Ų buried · 19 hydrogen bonds · protein-protein
- F–I · 1632 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5XGO · The Ferritin E-Domain: Toward Understanding Its Role in Protein Cage Assembly Through the… · the same entry in another collection · chain K against K, 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 P0ABT2
- Every structure of UniProt P0ABD3
- Elsewhere: RCSB PDB 5XGO · PDBe 5XGO · UniProt P0ABT2 · UniProt P0ABD3
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