MolNFT v1 · #126082 · protein
Humanized archaeal ferritin
5LS9 · Ferritin, putative: “Humanized archaeal ferritin”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.61). MolNFT v1 #126082 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LS9
- Type
- protein
- Length
- 1,963 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin, putative
- UniProt
- O29424
- Ligands
- MG
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, L | Ferritin, putative | protein | 164 | 78% helix, 1% strand | O29424 |
| B, C, D, E, I | Ferritin, putative | protein | 163 | 77% helix, 1% strand | O29424 |
| F | Ferritin, putative | protein | 165 | 77% helix, 1% strand | O29424 |
| G, J | Ferritin, putative | protein | 164 | 76% helix, 1% strand | O29424 |
| H | Ferritin, putative | protein | 163 | 76% helix, 1% strand | O29424 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.61 | 0.76 | 53 | empty |
| 2 | 376 | 0.60 | 0.77 | 44 | empty |
| 3 | 363 | 0.59 | 0.76 | 41 | empty |
| 4 | 315 | 0.58 | 0.77 | 39 | empty |
| 5 | 264 | 0.56 | 0.77 | 38 | empty |
Interfaces
21 interfaces between chains.
- A–B · 1375 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1373 Ų buried · 21 hydrogen bonds · protein-protein
- K–L · 1361 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1359 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1322 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5LS9 · Humanized Archaeal ferritin · 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 O29424
- Elsewhere: RCSB PDB 5LS9 · PDBe 5LS9 · UniProt O29424
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