Research workbench
Iron and alpha-ketoglutarate-dependent endoperoxidase nvfi with different conformation
Analyse Iron and alpha-ketoglutarate-dependent endoperoxidase nvfi with different… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ENB
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nvfi
- Ligands
- OGA, H3X, FE
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nvfi | protein | 277 | 22% helix, 35% strand | — |
| B | Nvfi | protein | 271 | 23% helix, 33% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- H3X · Methyl (3'~{A}~{R},4'~{S},5'~{S},5~{A}~{S},6~{S},7~{S}, 9~{A}~{R})-1,1,3'~{A},4',5~{A},7,7'-heptamethyl-3,6'-bis(oxidanylidene)spiro[4,5,7,8,9,9~{a}-hexahydrobenzo[c]oxepine-6,2'-4,5-dihydro-3~{H}-1-benzofuran]-5'-carboxylate · ligand · chains A
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.78 | 0.87 | 45 | H3X, OGA, FE |
| 2 | 684 | 0.76 | 0.82 | 80 | empty |
| 3 | 363 | 0.73 | 0.84 | 37 | OGA, FE |
| 4 | 144 | 0.51 | 0.79 | 22 | empty |
| 5 | 65 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 784 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7ENB · iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with different conformation · 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
- Elsewhere: RCSB PDB 7ENB · PDBe 7ENB
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.