MolNFT v1 · #177310 · protein
Selenomethionine labeled FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase tqal
7EEH: “Selenomethionine labeled FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase tqal”. X-ray diffraction, 1 ligand (FE), 13 pockets (best druggability 0.82). MolNFT v1 #177310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EEH
- Type
- protein
- Length
- 1,084 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tqal
- UniProt
- Q8X0D9
- Ligands
- FE
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tqal | protein | 270 | 23% helix, 32% strand | Q8X0D9 |
| B, C | Tqal | protein | 272 | 25% helix, 33% strand | Q8X0D9 |
| D | Tqal | protein | 270 | 23% helix, 32% strand | Q8X0D9 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.82 | 0.86 | 57 | empty |
| 2 | 775 | 0.78 | 0.82 | 53 | empty |
| 3 | 313 | 0.65 | 0.80 | 32 | TRS |
| 4 | 338 | 0.63 | 0.79 | 35 | TRS, FE |
| 5 | 319 | 0.63 | 0.79 | 30 | TRS, FE |
Interfaces
4 interfaces between chains.
- B–C · 874 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 689 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 656 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 584 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 7EEH · Selenomethionine labeled Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TqaL · 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 Q8X0D9
- Elsewhere: RCSB PDB 7EEH · PDBe 7EEH · UniProt Q8X0D9
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