Research workbench
Crystal structure of phthalate dioxygenase from comamonas testosteroni KF1
Analyse Crystal structure of phthalate 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
- 7FJL
- Type
- protein
- Length
- 2,459 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rieske (2FE-2S) domain protein
- UniProt
- B7WQT1
- Ligands
- FES, SRT, FE2
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Rieske (2FE-2S) domain protein | protein | 412 | 23% helix, 28% strand | B7WQT1 |
| C, E | Rieske (2FE-2S) domain protein | protein | 407 | 23% helix, 28% strand | B7WQT1 |
| F | Rieske (2FE-2S) domain protein | protein | 409 | 24% helix, 28% strand | B7WQT1 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, B, C, D, E, F
- SRT · S,R meso-tartaric acid · ligand · 5 copies · chains B, C, D, E, F
- FE2 · Fe (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 16 copies · chains B, E, A, C, F, D
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.79 | 0.91 | 34 | empty |
| 2 | 258 | 0.78 | 0.91 | 35 | empty |
| 3 | 242 | 0.78 | 0.91 | 33 | empty |
| 4 | 270 | 0.78 | 0.90 | 39 | empty |
| 5 | 271 | 0.77 | 0.89 | 39 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1364 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1363 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 1349 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 1346 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1345 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7FJL · Crystal Structure of phthalate 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 B7WQT1
- Elsewhere: RCSB PDB 7FJL · PDBe 7FJL · UniProt B7WQT1
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