MolNFT v1 · #72178 · protein
Crystal structure of a putative aromatic-ring hydroxylating dioxygenase (TM1040_3219) from silicibacter sp. TM1040 at 1.80 a resolution
3N0Q: “Crystal structure of a putative aromatic-ring hydroxylating dioxygenase (TM1040_3219) from silicibacter sp.…”. X-ray diffraction, 3 ligands (FES, NI, CL), 3 pockets (best druggability 0.79). MolNFT v1 #72178 on GenesisL1: 3D…
- PDB
- 3N0Q
- Type
- protein
- Length
- 402 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aromatic-ring hydroxylating dioxygenase
- UniProt
- Q1GMC3
- Ligands
- FES, NI, CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aromatic-ring hydroxylating dioxygenase | protein | 402 | 30% helix, 25% strand | Q1GMC3 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.79 | 0.99 | 28 | CL, TRS |
| 2 | 124 | 0.45 | 0.77 | 19 | empty |
| 3 | 57 | 0.39 | 0.80 | 17 | empty |
Modifications
Observed in the structure: 6 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3N0Q · Crystal structure of a Putative aromatic-ring hydroxylating dioxygenase (TM1040_3219)… · 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 Q1GMC3
- Elsewhere: RCSB PDB 3N0Q · PDBe 3N0Q · UniProt Q1GMC3
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