Research workbench
Structure of H200N variant of homoprotocatechuate 2,3-dioxygenase from B.FUSCUM in complex with 4-nitrocatechol at 1.57 ang resolution
Analyse Structure of H200N 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
- 4Z6W
- Type
- protein
- Length
- 1,426 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoprotocatechuate 2,3-dioxygenase
- UniProt
- Q45135
- Ligands
- 4NC, FE2, CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoprotocatechuate 2,3-dioxygenase | protein | 355 | 17% helix, 34% strand | Q45135 |
| B, D | Homoprotocatechuate 2,3-dioxygenase | protein | 359 | 18% helix, 35% strand | Q45135 |
| C | Homoprotocatechuate 2,3-dioxygenase | protein | 353 | 17% helix, 35% strand | Q45135 |
Ligands and binding sites
- 4NC · 4-nitrocatechol · ligand · 4 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B, D
- P6G · Hexaethylene glycol · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.85 | 0.94 | 44 | empty |
| 2 | 369 | 0.84 | 0.93 | 47 | empty |
| 3 | 109 | 0.79 | 0.98 | 24 | empty |
| 4 | 67 | 0.73 | 0.98 | 29 | empty |
| 5 | 57 | 0.69 | 0.97 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1675 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 1652 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1635 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1276 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4Z6W · Structure of H200N 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 4Z6W · PDBe 4Z6W · UniProt Q45135
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