Research workbench
Crystal structure of phthalate dioxygenase in complex with phthalate
Analyse Crystal structure of phthalate dioxygenase in complex with phthalate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V25
- Type
- protein
- Length
- 2,446 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, PHT, FE2
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Rieske (2FE-2S) domain protein | protein | 423 | 22% helix, 28% strand | B7WQT1 |
| A | Rieske (2FE-2S) domain protein | protein | 407 | 22% helix, 28% strand | B7WQT1 |
| C | Rieske (2FE-2S) domain protein | protein | 407 | 22% helix, 29% strand | B7WQT1 |
| D | Rieske (2FE-2S) domain protein | protein | 405 | 23% helix, 29% strand | B7WQT1 |
| E | Rieske (2FE-2S) domain protein | protein | 395 | 23% helix, 29% strand | B7WQT1 |
| F | Rieske (2FE-2S) domain protein | protein | 409 | 22% helix, 26% strand | B7WQT1 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains B, A, C, D, E, F
- PHT · Phthalic acid · ligand · chains B
- FE2 · Fe (II) ion · metal · 6 copies · chains B, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.79 | 0.91 | 32 | empty |
| 2 | 269 | 0.78 | 0.90 | 37 | empty |
| 3 | 114 | 0.78 | 0.97 | 32 | PHT |
| 4 | 172 | 0.78 | 0.94 | 35 | FE2 |
| 5 | 231 | 0.77 | 0.91 | 33 | empty |
Interfaces
12 interfaces between chains.
- A–E · 1422 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 1407 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1387 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1337 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1335 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7V25 · Crystal Structure of phthalate dioxygenase in complex with phthalate · 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 B7WQT1
- Elsewhere: RCSB PDB 7V25 · PDBe 7V25 · UniProt B7WQT1
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