Research workbench
Heavy chain ferritin with C-terminal EBNA1 epitope
Analyse Heavy chain ferritin with C-terminal EBNA1 epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KE3
- Type
- protein
- Length
- 2,001 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy CHAIN,EPSTEIN-barr nuclear antigen 1
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- FE
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Ferritin heavy CHAIN,EPSTEIN-barr nuclear antigen 1 (EC 1.16.3.1) | protein | 166 | 75% helix, 1% strand | P02794 |
| C, E, F, G, H, I, J, K, L | Ferritin heavy CHAIN,EPSTEIN-barr nuclear antigen 1 (EC 1.16.3.1) | protein | 167 | 75% helix, 1% strand | P02794 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 20 copies · chains A, H, B, D, J, C, L, K, G, E, I, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.98 | 16 | TRS |
| 2 | 84 | 0.75 | 0.97 | 17 | TRS |
| 3 | 64 | 0.73 | 0.98 | 14 | TRS |
| 4 | 57 | 0.72 | 0.98 | 13 | TRS |
| 5 | 59 | 0.71 | 0.97 | 14 | TRS |
Interfaces
25 interfaces between chains.
- A–B · 1551 Ų buried · 39 hydrogen bonds · protein-protein
- I–J · 1548 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1544 Ų buried · 37 hydrogen bonds · protein-protein
- K–L · 1541 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 1531 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 7KE3 · Heavy chain ferritin with C-terminal EBNA1 epitope · 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 7KE3 · PDBe 7KE3 · UniProt P02794
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