Research workbench
Crystal structure of FMN-binding protein (YP_005476) from thermus thermophilus with bound 1-cyclohex-2-enone
Analyse Crystal structure of FMN-binding protein (YP_005476) from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZOH
- Type
- protein
- Length
- 712 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavoredoxin
- UniProt
- Q72HI0
- Ligands
- A2Q, FMN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Flavoredoxin | protein | 178 | 12% helix, 46% strand | Q72HI0 |
Ligands and binding sites
- A2Q · cyclohex-2-en-1-one · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.77 | 0.99 | 20 | empty |
| 2 | 78 | 0.76 | 0.99 | 21 | empty |
| 3 | 802 | 0.70 | 0.76 | 62 | empty |
| 4 | 281 | 0.61 | 0.79 | 38 | A2Q, FMN |
| 5 | 302 | 0.61 | 0.79 | 40 | A2Q, FMN |
Interfaces
5 interfaces between chains.
- C–D · 3823 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3764 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZOH · Crystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound… · 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 Q72HI0
- Elsewhere: RCSB PDB 3ZOH · PDBe 3ZOH · UniProt Q72HI0
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