Research workbench
Cubic-shaped crystal of tmftn mutant-T4FY stimulated by mg
Analyse Cubic-shaped crystal of tmftn mutant-T4FY stimulated by mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LS3
- Type
- protein
- Length
- 1,310 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, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E, A, C, D, G | Ferritin (EC 1.16.3.2) | protein | 164 | 77% helix, 1% strand | Q9X0L2 |
| F, H | Ferritin (EC 1.16.3.2) | protein | 163 | 75% helix, 1% strand | Q9X0L2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 15 copies · chains B, E, A, C, D, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains B, A, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.72 | 0.86 | 30 | empty |
| 2 | 264 | 0.72 | 0.86 | 30 | empty |
| 3 | 243 | 0.71 | 0.85 | 29 | empty |
| 4 | 297 | 0.70 | 0.83 | 35 | empty |
| 5 | 380 | 0.62 | 0.77 | 44 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1281 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1280 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1275 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1263 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 516 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6LS3 · cubic-shaped crystal of TmFtn mutant-T4FY stimulated by Mg · the same entry in another collection · chain B against B, 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 6LS3 · PDBe 6LS3 · UniProt Q9X0L2
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