MolNFT v1 · #165502 · protein
Crystal structure of thermotoga maritima A42V E65D ferritin
6TXJ: “Crystal structure of thermotoga maritima A42V E65D ferritin”. X-ray diffraction, 3 ligands (LFA, FE, SO4), 19 pockets (best druggability 0.73). MolNFT v1 #165502 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TXJ
- Type
- protein
- Length
- 1,309 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.2
- UniProt
- Q9X0L2
- Ligands
- LFA, FE, SO4
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Ferritin (EC 1.16.3.2) | protein | 163 | 79% helix, 1% strand | Q9X0L2 |
| B, C, E, F, H | Ferritin (EC 1.16.3.2) | protein | 164 | 78% helix, 1% strand | Q9X0L2 |
Ligands and binding sites
- LFA · Eicosane · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 35 copies · chains A, B, D, E, C, F, G, H
- GOL · Glycerol · additive · 7 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.73 | 0.86 | 24 | LFA |
| 2 | 237 | 0.72 | 0.87 | 24 | LFA |
| 3 | 286 | 0.72 | 0.85 | 29 | LFA |
| 4 | 286 | 0.70 | 0.84 | 34 | LFA, SO4 |
| 5 | 466 | 0.70 | 0.80 | 41 | SO4 |
Interfaces
12 interfaces between chains.
- E–F · 1269 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1265 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1257 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1239 Ų buried · 24 hydrogen bonds · protein-protein
- E–G · 511 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6TXJ · Crystal structure of thermotoga maritima A42V E65D 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 Q9X0L2
- Elsewhere: RCSB PDB 6TXJ · PDBe 6TXJ · UniProt Q9X0L2
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