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Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution
Analyse Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GHF
- Type
- protein
- Length
- 1,424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.67
- Source
- Brevibacterium fuscum
- Molecule
- Homoprotocatechuate 2,3-dioxygenase
- EC
- 1.13.11.15
- UniProt
- Q45135
- Ligands
- 4NC, FE2, CA, CL, OXY
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.67 · 3 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoprotocatechuate 2,3-dioxygenase (EC 1.13.11.15) | protein | 355 | 17% helix, 34% strand | Q45135 |
| B, D | Homoprotocatechuate 2,3-dioxygenase (EC 1.13.11.15) | protein | 359 | 17% helix, 35% strand | Q45135 |
| C | Homoprotocatechuate 2,3-dioxygenase (EC 1.13.11.15) | protein | 351 | 17% helix, 35% strand | Q45135 |
Ligands and binding sites
- 4NC · 4-nitrocatechol · ligand · 3 copies · chains A, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 2 copies · chains C, D
- P6G · Hexaethylene glycol · additive · 5 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.84 | 0.89 | 76 | empty |
| 2 | 598 | 0.83 | 0.88 | 65 | PG4 |
| 3 | 111 | 0.79 | 0.98 | 23 | empty |
| 4 | 59 | 0.72 | 0.98 | 25 | empty |
| 5 | 63 | 0.71 | 0.97 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1682 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1670 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1666 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1272 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GHF · Structure of Y257F variant of homoprotocatechuate 2,3-dioxygenase from B.FUSCUM in… · 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 Q45135
- Elsewhere: RCSB PDB 4GHF · PDBe 4GHF · UniProt Q45135
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