Research workbench
Engineering a closed form of the archaeoglobus fulgidus ferritin by site directed mutagenesis
Analyse Engineering a closed form of the archaeoglobus fulgidus ferritin by site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KX9
- Type
- protein
- Length
- 3,913 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- UniProt
- O29424
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Ferritin | protein | 163 | 78% helix, 1% strand | O29424 |
| D | Ferritin | protein | 164 | 77% helix, 1% strand | O29424 |
Ligands and binding sites
- GOL · Glycerol · additive · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
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 | 1061 | 0.76 | 0.79 | 134 | empty |
| 2 | 262 | 0.61 | 0.80 | 40 | empty |
| 3 | 260 | 0.58 | 0.78 | 32 | empty |
| 4 | 212 | 0.58 | 0.80 | 37 | empty |
| 5 | 214 | 0.57 | 0.80 | 41 | empty |
Interfaces
72 interfaces between chains.
- A–B · 1324 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 1317 Ų buried · 23 hydrogen bonds · protein-protein
- W–X · 1316 Ų buried · 22 hydrogen bonds · protein-protein
- M–N · 1315 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1312 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3KX9 · Engineering a closed form of the Archaeoglobus fulgidus ferritin by site directed… · the same entry in another collection · chain I against I, 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 O29424
- Elsewhere: RCSB PDB 3KX9 · PDBe 3KX9 · UniProt O29424
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