Research workbench
Crystal structure of the as isolated ferritin from the hyperthermophilic archaeal anaerobe pyrococcus furiosus
Analyse Crystal structure of the as isolated ferritin from the hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JD6
- Type
- protein
- Length
- 6,012 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin homolog
- UniProt
- Q8U2T8
- Ligands
- FE, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z | Ferritin homolog | protein | 167 | 75% helix, 1% strand | Q8U2T8 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 36 copies · chains 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
- SO4 · Sulfate ion · ion · 40 copies · chains 1, 5, 2, 3, Y, 4, 8, 6, 0, 7, 9, A, C, D, B, E, G, U, F, X, I, H, K, J, R, M, O, P, L, Q, S, T, V, W, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.84 | 0.95 | 29 | empty |
| 2 | 226 | 0.84 | 0.95 | 28 | empty |
| 3 | 245 | 0.83 | 0.94 | 31 | empty |
| 4 | 246 | 0.82 | 0.93 | 32 | empty |
| 5 | 226 | 0.82 | 0.94 | 30 | empty |
Interfaces
95 interfaces between chains.
- C–U · 1618 Ų buried · 23 hydrogen bonds · protein-protein
- 6–O · 1607 Ų buried · 19 hydrogen bonds · protein-protein
- D–V · 1605 Ų buried · 24 hydrogen bonds · protein-protein
- 8–Q · 1603 Ų buried · 21 hydrogen bonds · protein-protein
- G–Y · 1596 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2JD6 · Crystal Structure of the as isolated Ferritin from the Hyperthermophilic Archaeal… · the same entry in another collection · chain X against X, 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 Q8U2T8
- Elsewhere: RCSB PDB 2JD6 · PDBe 2JD6 · UniProt Q8U2T8
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