Research workbench
Crystal structure of terephthalate dioxygenase from comamonas testosteroni KF1
Analyse Crystal structure of terephthalate dioxygenase from comamonas testosteroni KF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VJU
- Type
- protein
- Length
- 1,609 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rieske (2FE-2S) domain protein; Aromatic-ring-hydroxylating dioxygenase beta subunit
- UniProt
- B7WRJ9, B7WRJ8
- Ligands
- FES, FE2, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rieske (2FE-2S) domain protein | protein | 378 | 28% helix, 28% strand | B7WRJ9 |
| B, F | Aromatic-ring-hydroxylating dioxygenase beta subunit | protein | 153 | 27% helix, 44% strand | B7WRJ8 |
| C | Rieske (2FE-2S) domain protein | protein | 393 | 27% helix, 29% strand | B7WRJ9 |
| D | Aromatic-ring-hydroxylating dioxygenase beta subunit | protein | 154 | 27% helix, 44% strand | B7WRJ8 |
| E | Rieske (2FE-2S) domain protein | protein | 378 | 26% helix, 27% strand | B7WRJ9 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
- FE2 · Fe (II) ion · metal · 3 copies · chains A, C, E
- PO4 · Phosphate ion · ion · 10 copies · chains A, E, B, C, F, D
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, C, D, E, F, B
- GOL · Glycerol · additive · 3 copies · chains A, D, F, E
- PG4 · Tetraethylene glycol · additive · chains A
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 | 288 | 0.83 | 0.94 | 57 | empty |
| 2 | 948 | 0.81 | 0.83 | 116 | PEG, GOL, PO4 |
| 3 | 876 | 0.81 | 0.83 | 105 | PEG, PO4, GOL |
| 4 | 1164 | 0.79 | 0.81 | 122 | PEG, GOL, PO4 |
| 5 | 602 | 0.76 | 0.83 | 60 | FE2, PO4 |
Interfaces
12 interfaces between chains.
- C–D · 1694 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1693 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1633 Ų buried · 34 hydrogen bonds · protein-protein
- C–E · 1376 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1350 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7VJU · Crystal Structure of terephthalate dioxygenase from Comamonas testosteroni KF1 · 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 B7WRJ9
- Every structure of UniProt B7WRJ8
- Elsewhere: RCSB PDB 7VJU · PDBe 7VJU · UniProt B7WRJ9 · UniProt B7WRJ8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.