Research workbench
Heavy chain ferritin with N-terminal EBNA1 epitope
Analyse Heavy chain ferritin with N-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
- 7KE5
- Type
- protein
- Length
- 2,046 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epstein-barr nuclear antigen 1,FERRITIN heavy chain
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- FE
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, G, I, L | Epstein-barr nuclear antigen 1,FERRITIN heavy chain (EC 1.16.3.1) | protein | 172 | 73% helix, 1% strand | P02794 |
| C, E, F, H, J, K | Epstein-barr nuclear antigen 1,FERRITIN heavy chain (EC 1.16.3.1) | protein | 169 | 75% helix, 1% strand | P02794 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 16 copies · chains A, H, B, C, J, L, D, G, E, I, F, K
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.77 | 0.95 | 19 | TRS |
| 2 | 76 | 0.77 | 0.99 | 16 | TRS |
| 3 | 88 | 0.76 | 0.97 | 16 | TRS |
| 4 | 87 | 0.76 | 0.97 | 17 | TRS |
| 5 | 63 | 0.75 | 0.99 | 13 | TRS |
Interfaces
25 interfaces between chains.
- K–L · 1527 Ų buried · 33 hydrogen bonds · protein-protein
- I–J · 1521 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1504 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1500 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1456 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7KE5 · Heavy chain ferritin with N-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 7KE5 · PDBe 7KE5 · UniProt P02794
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