MolNFT v1 · #69695 · protein
Crystal structure of putative riboflavin biosynthesis protein (YP_001092907.1) from shewanella sp. pv-4 at 2.12 a resolution
3KY8: “Crystal structure of putative riboflavin biosynthesis protein (YP_001092907.1) from shewanella sp. pv-4 at…”. X-ray diffraction, 2 ligands (UNL, SO4), 6 pockets (best druggability 0.69). MolNFT v1 #69695 on GenesisL1: 3D structure…
- PDB
- 3KY8
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative riboflavin biosynthesis protein
- UniProt
- A3QB00
- Ligands
- UNL, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative riboflavin biosynthesis protein | protein | 184 | 21% helix, 33% strand | A3QB00 |
| B | Putative riboflavin biosynthesis protein | protein | 177 | 23% helix, 32% strand | A3QB00 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.69 | 0.79 | 47 | UNL, SO4 |
| 2 | 531 | 0.65 | 0.76 | 41 | UNL, SO4 |
| 3 | 103 | 0.52 | 0.82 | 22 | empty |
| 4 | 90 | 0.41 | 0.78 | 21 | empty |
| 5 | 77 | 0.32 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1241 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3KY8 · Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from… · 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 A3QB00
- Elsewhere: RCSB PDB 3KY8 · PDBe 3KY8 · UniProt A3QB00
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