MolNFT v1 · #176811 · protein
Crystal structure of tmftn with calcium ions
7DYA · Ferritin: “Crystal structure of tmftn with calcium ions”. X-ray diffraction, 2 ligands (FE, CA), 16 pockets (best druggability 0.76). MolNFT v1 #176811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DYA
- Type
- protein
- Length
- 1,312 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
- FE, CA
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A, B, C, D, E, F, G | Ferritin (EC 1.16.3.2) | protein | 164 | 77% helix, 0% strand | Q9X0L2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 16 copies · chains H, A, B, C, D, E, F, G
- CA · Calcium ion · metal · 9 copies · chains H, A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.76 | 0.84 | 33 | empty |
| 2 | 258 | 0.71 | 0.85 | 26 | empty |
| 3 | 250 | 0.70 | 0.85 | 27 | empty |
| 4 | 713 | 0.70 | 0.77 | 76 | empty |
| 5 | 270 | 0.69 | 0.83 | 30 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1208 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1204 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 1188 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 545 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 536 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7DYA · Crystal structure of TmFtn with calcium ions · the same entry in another collection · chain H against H, 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 7DYA · PDBe 7DYA · UniProt Q9X0L2
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