MolNFT v1 · #112832 · protein
Crystal structure of hydroquinone 1,2-dioxygenase pnpcd in complex with FE3+
4ZXC · Hydroquinone dioxygenase small subunit: “Crystal structure of hydroquinone 1,2-dioxygenase pnpcd in complex with FE3+”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.86). MolNFT v1 #112832 on GenesisL1: 3D…
- PDB
- 4ZXC
- Type
- protein
- Length
- 1,948 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroquinone dioxygenase small subunit; Hydroquinone dioxygenase large subunit
- UniProt
- C1I210, C1I209
- Ligands
- FE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, C, B | Hydroquinone dioxygenase small subunit | protein | 163 | 8% helix, 52% strand | C1I210 |
| W, Z, Y, X | Hydroquinone dioxygenase large subunit | protein | 324 | 16% helix, 34% strand | C1I209 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains W, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.86 | 0.87 | 107 | empty |
| 2 | 1177 | 0.85 | 0.86 | 102 | empty |
| 3 | 78 | 0.75 | 0.97 | 18 | empty |
| 4 | 72 | 0.72 | 0.96 | 25 | empty |
| 5 | 450 | 0.68 | 0.79 | 55 | empty |
Interfaces
13 interfaces between chains.
- D–Z · 3055 Ų buried · 54 hydrogen bonds · protein-protein
- A–W · 3055 Ų buried · 54 hydrogen bonds · protein-protein
- C–Y · 3023 Ų buried · 53 hydrogen bonds · protein-protein
- B–X · 2980 Ų buried · 55 hydrogen bonds · protein-protein
- W–X · 1180 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4ZXC · Crystal Structure of hydroqui 1,2-dioxygenase PnpCD in complex with Fe3+ · 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 C1I210
- Every structure of UniProt C1I209
- Elsewhere: RCSB PDB 4ZXC · PDBe 4ZXC · UniProt C1I210 · UniProt C1I209
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