Research workbench
Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from arthrobacter sp. FB24 at 2.33 a resolution
Analyse Crystal structure of protein of unknown function with ferritin-like fold… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EZ0
- Type
- protein
- Length
- 847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein with ferritin-like fold
- UniProt
- A0JYP2
- Ligands
- UNL
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein with ferritin-like fold | protein | 216 | 81% helix, 0% strand | A0JYP2 |
| B | Uncharacterized protein with ferritin-like fold | protein | 213 | 85% helix, 0% strand | A0JYP2 |
| C | Uncharacterized protein with ferritin-like fold | protein | 208 | 81% helix, 0% strand | A0JYP2 |
| D | Uncharacterized protein with ferritin-like fold | protein | 210 | 83% helix, 0% strand | A0JYP2 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.87 | 0.93 | 52 | UNL |
| 2 | 524 | 0.86 | 0.92 | 52 | UNL |
| 3 | 633 | 0.85 | 0.89 | 58 | UNL |
| 4 | 696 | 0.85 | 0.88 | 59 | UNL |
| 5 | 749 | 0.78 | 0.83 | 68 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1025 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1024 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3EZ0 · Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1)… · 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 A0JYP2
- Elsewhere: RCSB PDB 3EZ0 · PDBe 3EZ0 · UniProt A0JYP2
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